Starting phenix.real_space_refine on Wed Jun 11 04:20:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ask_11895/06_2025/7ask_11895.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ask_11895/06_2025/7ask_11895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ask_11895/06_2025/7ask_11895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ask_11895/06_2025/7ask_11895.map" model { file = "/net/cci-nas-00/data/ceres_data/7ask_11895/06_2025/7ask_11895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ask_11895/06_2025/7ask_11895.cif" } resolution = 4.3 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 7744 2.51 5 N 2170 2.21 5 O 2302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12285 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 12257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1523, 12257 Classifications: {'peptide': 1523} Link IDs: {'CIS': 45, 'PCIS': 3, 'PTRANS': 50, 'TRANS': 1424} Chain breaks: 15 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.41, per 1000 atoms: 0.60 Number of scatterers: 12285 At special positions: 0 Unit cell: (156.96, 114.45, 160.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 2 15.00 Mg 1 11.99 O 2302 8.00 N 2170 7.00 C 7744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB TYR F 296 " pdb=" CB TYR F 305 " pdb=" CB ILE F1155 " pdb=" CB ARG F1697 " Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 47.4% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'F' and resid 1 through 16 removed outlier: 4.871A pdb=" N ILE F 9 " --> pdb=" O TYR F 5 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 38 removed outlier: 3.631A pdb=" N THR F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 75 removed outlier: 3.947A pdb=" N ASP F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 109 removed outlier: 3.923A pdb=" N LEU F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY F 103 " --> pdb=" O LYS F 99 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA F 104 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA F 107 " --> pdb=" O GLY F 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 130 removed outlier: 3.822A pdb=" N VAL F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR F 129 " --> pdb=" O VAL F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 144 removed outlier: 3.584A pdb=" N LEU F 143 " --> pdb=" O PHE F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 161 Processing helix chain 'F' and resid 177 through 188 removed outlier: 3.783A pdb=" N GLN F 181 " --> pdb=" O ILE F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 228 removed outlier: 4.210A pdb=" N GLU F 228 " --> pdb=" O MET F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 256 removed outlier: 4.032A pdb=" N TRP F 255 " --> pdb=" O TYR F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 287 removed outlier: 3.579A pdb=" N GLN F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA F 276 " --> pdb=" O ASN F 272 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE F 277 " --> pdb=" O PRO F 273 " (cutoff:3.500A) Proline residue: F 281 - end of helix Processing helix chain 'F' and resid 671 through 675 Processing helix chain 'F' and resid 686 through 695 removed outlier: 3.842A pdb=" N HIS F 691 " --> pdb=" O VAL F 687 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA F 692 " --> pdb=" O ASN F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 764 removed outlier: 4.540A pdb=" N ASP F 744 " --> pdb=" O THR F 740 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE F 749 " --> pdb=" O ARG F 745 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN F 761 " --> pdb=" O LYS F 757 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU F 762 " --> pdb=" O ARG F 758 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE F 764 " --> pdb=" O SER F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 776 through 779 Processing helix chain 'F' and resid 780 through 792 removed outlier: 3.798A pdb=" N LEU F 784 " --> pdb=" O THR F 780 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 787 " --> pdb=" O PRO F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 810 through 815 Processing helix chain 'F' and resid 816 through 823 removed outlier: 3.782A pdb=" N LYS F 820 " --> pdb=" O LYS F 816 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP F 823 " --> pdb=" O SER F 819 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 845 removed outlier: 3.680A pdb=" N PHE F 840 " --> pdb=" O VAL F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 853 through 860 removed outlier: 3.587A pdb=" N ARG F 858 " --> pdb=" O LEU F 854 " (cutoff:3.500A) Processing helix chain 'F' and resid 866 through 901 removed outlier: 3.909A pdb=" N LEU F 873 " --> pdb=" O ALA F 869 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU F 878 " --> pdb=" O ARG F 874 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE F 880 " --> pdb=" O VAL F 876 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N HIS F 884 " --> pdb=" O PHE F 880 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU F 889 " --> pdb=" O ILE F 885 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL F 893 " --> pdb=" O LEU F 889 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 896 " --> pdb=" O ARG F 892 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU F 898 " --> pdb=" O VAL F 894 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU F 899 " --> pdb=" O LYS F 895 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN F 900 " --> pdb=" O LEU F 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 907 removed outlier: 3.866A pdb=" N ARG F 905 " --> pdb=" O TRP F 901 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU F 906 " --> pdb=" O ARG F 902 " (cutoff:3.500A) Processing helix chain 'F' and resid 921 through 932 Processing helix chain 'F' and resid 946 through 955 Processing helix chain 'F' and resid 962 through 976 removed outlier: 3.536A pdb=" N LYS F 966 " --> pdb=" O SER F 962 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP F 968 " --> pdb=" O TYR F 964 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN F 969 " --> pdb=" O ASN F 965 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS F 970 " --> pdb=" O LYS F 966 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG F 973 " --> pdb=" O GLN F 969 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TRP F 974 " --> pdb=" O CYS F 970 " (cutoff:3.500A) Processing helix chain 'F' and resid 1001 through 1007 removed outlier: 3.855A pdb=" N MET F1005 " --> pdb=" O GLN F1001 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS F1007 " --> pdb=" O ILE F1003 " (cutoff:3.500A) Processing helix chain 'F' and resid 1028 through 1037 removed outlier: 4.968A pdb=" N ASP F1034 " --> pdb=" O ARG F1030 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE F1035 " --> pdb=" O GLU F1031 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F1036 " --> pdb=" O LEU F1032 " (cutoff:3.500A) Processing helix chain 'F' and resid 1053 through 1055 No H-bonds generated for 'chain 'F' and resid 1053 through 1055' Processing helix chain 'F' and resid 1056 through 1057 No H-bonds generated for 'chain 'F' and resid 1056 through 1057' Processing helix chain 'F' and resid 1059 through 1066 removed outlier: 3.836A pdb=" N ARG F1066 " --> pdb=" O LYS F1062 " (cutoff:3.500A) Processing helix chain 'F' and resid 1082 through 1092 removed outlier: 4.597A pdb=" N VAL F1086 " --> pdb=" O ILE F1082 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG F1092 " --> pdb=" O ASP F1088 " (cutoff:3.500A) Processing helix chain 'F' and resid 1127 through 1137 Processing helix chain 'F' and resid 1140 through 1145 removed outlier: 3.715A pdb=" N VAL F1144 " --> pdb=" O TYR F1140 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F1145 " --> pdb=" O THR F1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1140 through 1145' Processing helix chain 'F' and resid 1155 through 1162 removed outlier: 3.714A pdb=" N ASN F1161 " --> pdb=" O SER F1157 " (cutoff:3.500A) Processing helix chain 'F' and resid 1166 through 1171 removed outlier: 3.613A pdb=" N ILE F1170 " --> pdb=" O VAL F1166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F1171 " --> pdb=" O TRP F1167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1166 through 1171' Processing helix chain 'F' and resid 1188 through 1206 removed outlier: 3.509A pdb=" N TRP F1194 " --> pdb=" O GLN F1190 " (cutoff:3.500A) Processing helix chain 'F' and resid 1271 through 1278 removed outlier: 3.947A pdb=" N GLN F1276 " --> pdb=" O ALA F1272 " (cutoff:3.500A) Processing helix chain 'F' and resid 1290 through 1298 removed outlier: 4.087A pdb=" N GLU F1295 " --> pdb=" O VAL F1291 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS F1296 " --> pdb=" O SER F1292 " (cutoff:3.500A) Processing helix chain 'F' and resid 1313 through 1331 removed outlier: 4.969A pdb=" N GLN F1321 " --> pdb=" O THR F1317 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET F1323 " --> pdb=" O ARG F1319 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU F1324 " --> pdb=" O ALA F1320 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU F1326 " --> pdb=" O LEU F1322 " (cutoff:3.500A) Proline residue: F1327 - end of helix removed outlier: 3.568A pdb=" N TYR F1330 " --> pdb=" O GLU F1326 " (cutoff:3.500A) Processing helix chain 'F' and resid 1342 through 1349 removed outlier: 4.151A pdb=" N GLU F1346 " --> pdb=" O ALA F1342 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA F1347 " --> pdb=" O ARG F1343 " (cutoff:3.500A) Processing helix chain 'F' and resid 1349 through 1358 removed outlier: 4.082A pdb=" N TYR F1355 " --> pdb=" O ASN F1351 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP F1356 " --> pdb=" O ALA F1352 " (cutoff:3.500A) Processing helix chain 'F' and resid 1381 through 1401 removed outlier: 3.804A pdb=" N ARG F1391 " --> pdb=" O GLU F1387 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F1392 " --> pdb=" O SER F1388 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F1394 " --> pdb=" O LEU F1390 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN F1395 " --> pdb=" O ARG F1391 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS F1396 " --> pdb=" O THR F1392 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN F1398 " --> pdb=" O ALA F1394 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU F1399 " --> pdb=" O GLN F1395 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP F1400 " --> pdb=" O LYS F1396 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU F1401 " --> pdb=" O LEU F1397 " (cutoff:3.500A) Processing helix chain 'F' and resid 1403 through 1420 removed outlier: 3.682A pdb=" N ALA F1408 " --> pdb=" O LEU F1404 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA F1409 " --> pdb=" O GLU F1405 " (cutoff:3.500A) Processing helix chain 'F' and resid 1420 through 1436 removed outlier: 3.849A pdb=" N HIS F1424 " --> pdb=" O LEU F1420 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F1428 " --> pdb=" O HIS F1424 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN F1429 " --> pdb=" O LEU F1425 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU F1432 " --> pdb=" O LEU F1428 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN F1435 " --> pdb=" O GLN F1431 " (cutoff:3.500A) Processing helix chain 'F' and resid 1475 through 1488 removed outlier: 3.569A pdb=" N ILE F1479 " --> pdb=" O ILE F1475 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU F1480 " --> pdb=" O ARG F1476 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN F1481 " --> pdb=" O GLU F1477 " (cutoff:3.500A) Processing helix chain 'F' and resid 1503 through 1521 Processing helix chain 'F' and resid 1527 through 1553 removed outlier: 3.692A pdb=" N ARG F1534 " --> pdb=" O LEU F1530 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE F1535 " --> pdb=" O TYR F1531 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA F1539 " --> pdb=" O ILE F1535 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS F1547 " --> pdb=" O GLU F1543 " (cutoff:3.500A) Processing helix chain 'F' and resid 1588 through 1592 removed outlier: 3.779A pdb=" N GLU F1591 " --> pdb=" O VAL F1588 " (cutoff:3.500A) Processing helix chain 'F' and resid 1602 through 1617 removed outlier: 4.207A pdb=" N VAL F1606 " --> pdb=" O GLU F1602 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F1615 " --> pdb=" O GLU F1611 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU F1616 " --> pdb=" O ASP F1612 " (cutoff:3.500A) Processing helix chain 'F' and resid 1620 through 1627 removed outlier: 4.045A pdb=" N GLN F1626 " --> pdb=" O LEU F1622 " (cutoff:3.500A) Processing helix chain 'F' and resid 1637 through 1650 removed outlier: 3.615A pdb=" N ARG F1646 " --> pdb=" O ALA F1642 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU F1647 " --> pdb=" O HIS F1643 " (cutoff:3.500A) Processing helix chain 'F' and resid 1660 through 1664 Processing helix chain 'F' and resid 1683 through 1692 removed outlier: 4.009A pdb=" N GLN F1689 " --> pdb=" O THR F1685 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET F1690 " --> pdb=" O GLN F1686 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY F1692 " --> pdb=" O ARG F1688 " (cutoff:3.500A) Processing helix chain 'F' and resid 1713 through 1720 removed outlier: 4.017A pdb=" N ARG F1717 " --> pdb=" O ARG F1713 " (cutoff:3.500A) Processing helix chain 'F' and resid 1733 through 1749 removed outlier: 3.799A pdb=" N ASN F1737 " --> pdb=" O ASP F1733 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN F1747 " --> pdb=" O LEU F1743 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F1748 " --> pdb=" O TYR F1744 " (cutoff:3.500A) Processing helix chain 'F' and resid 1754 through 1769 Processing helix chain 'F' and resid 1775 through 1780 Processing helix chain 'F' and resid 1791 through 1800 removed outlier: 4.410A pdb=" N MET F1797 " --> pdb=" O GLU F1793 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY F1800 " --> pdb=" O GLN F1796 " (cutoff:3.500A) Processing helix chain 'F' and resid 1821 through 1825 removed outlier: 3.696A pdb=" N MET F1824 " --> pdb=" O GLN F1821 " (cutoff:3.500A) Processing helix chain 'F' and resid 1827 through 1831 Processing helix chain 'F' and resid 1841 through 1847 Processing helix chain 'F' and resid 1848 through 1850 No H-bonds generated for 'chain 'F' and resid 1848 through 1850' Processing helix chain 'F' and resid 1857 through 1867 removed outlier: 3.566A pdb=" N VAL F1865 " --> pdb=" O LEU F1861 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP F1867 " --> pdb=" O SER F1863 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 135 through 136 removed outlier: 3.669A pdb=" N TYR F 305 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG F 306 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS F 293 " --> pdb=" O ARG F 306 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE F 260 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP F 152 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE F 149 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE F 198 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE F 151 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N SER F 238 " --> pdb=" O HIS F 195 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL F 197 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 1105 through 1107 removed outlier: 6.757A pdb=" N VAL F1072 " --> pdb=" O LEU F1124 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N THR F1126 " --> pdb=" O VAL F1072 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR F1074 " --> pdb=" O THR F1126 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL F1179 " --> pdb=" O VAL F1150 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU F1152 " --> pdb=" O VAL F1179 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU F1181 " --> pdb=" O LEU F1152 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER F1041 " --> pdb=" O VAL F1218 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU F1220 " --> pdb=" O SER F1041 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL F1043 " --> pdb=" O LEU F1220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 1233 through 1236 removed outlier: 7.121A pdb=" N THR F1494 " --> pdb=" O ILE F1656 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N SER F1658 " --> pdb=" O THR F1494 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL F1496 " --> pdb=" O SER F1658 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1071 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: 3.76 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.42: 5288 1.42 - 1.81: 7130 1.81 - 2.20: 106 2.20 - 2.59: 0 2.59 - 2.98: 1 Bond restraints: 12525 Sorted by residual: bond pdb=" C ARG F1521 " pdb=" N TYR F1522 " ideal model delta sigma weight residual 1.335 2.980 -1.645 1.36e-02 5.41e+03 1.46e+04 bond pdb=" C TYR F1149 " pdb=" N VAL F1150 " ideal model delta sigma weight residual 1.331 1.724 -0.393 1.29e-02 6.01e+03 9.30e+02 bond pdb=" CA PRO F 304 " pdb=" C PRO F 304 " ideal model delta sigma weight residual 1.522 1.191 0.331 1.16e-02 7.43e+03 8.14e+02 bond pdb=" CA TYR F 305 " pdb=" C TYR F 305 " ideal model delta sigma weight residual 1.523 1.202 0.321 1.34e-02 5.57e+03 5.75e+02 bond pdb=" CA PHE F 259 " pdb=" C PHE F 259 " ideal model delta sigma weight residual 1.522 1.813 -0.291 1.24e-02 6.50e+03 5.51e+02 ... (remaining 12520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.67: 16641 8.67 - 17.34: 179 17.34 - 26.00: 56 26.00 - 34.67: 5 34.67 - 43.34: 6 Bond angle restraints: 16887 Sorted by residual: angle pdb=" O GLY F1051 " pdb=" C GLY F1051 " pdb=" N LYS F1052 " ideal model delta sigma weight residual 122.42 84.72 37.70 1.31e+00 5.83e-01 8.28e+02 angle pdb=" CA ASN F 303 " pdb=" C ASN F 303 " pdb=" N PRO F 304 " ideal model delta sigma weight residual 117.68 97.94 19.74 7.10e-01 1.98e+00 7.73e+02 angle pdb=" O ARG F1521 " pdb=" C ARG F1521 " pdb=" N TYR F1522 " ideal model delta sigma weight residual 122.22 90.29 31.93 1.17e+00 7.31e-01 7.45e+02 angle pdb=" O LEU F1136 " pdb=" C LEU F1136 " pdb=" N SER F1137 " ideal model delta sigma weight residual 122.08 148.00 -25.92 1.07e+00 8.73e-01 5.87e+02 angle pdb=" N ILE F1155 " pdb=" CA ILE F1155 " pdb=" CB ILE F1155 " ideal model delta sigma weight residual 111.50 150.54 -39.04 1.70e+00 3.46e-01 5.27e+02 ... (remaining 16882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.31: 7025 25.31 - 50.63: 391 50.63 - 75.94: 147 75.94 - 101.26: 15 101.26 - 126.57: 12 Dihedral angle restraints: 7590 sinusoidal: 3163 harmonic: 4427 Sorted by residual: dihedral pdb=" CA GLY F1784 " pdb=" C GLY F1784 " pdb=" N GLY F1785 " pdb=" CA GLY F1785 " ideal model delta harmonic sigma weight residual -180.00 -53.43 -126.57 0 5.00e+00 4.00e-02 6.41e+02 dihedral pdb=" CA ARG F1214 " pdb=" C ARG F1214 " pdb=" N ASP F1215 " pdb=" CA ASP F1215 " ideal model delta harmonic sigma weight residual 180.00 53.77 126.23 0 5.00e+00 4.00e-02 6.37e+02 dihedral pdb=" CA SER F 144 " pdb=" C SER F 144 " pdb=" N ALA F 145 " pdb=" CA ALA F 145 " ideal model delta harmonic sigma weight residual 180.00 56.28 123.72 0 5.00e+00 4.00e-02 6.12e+02 ... (remaining 7587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.858: 1817 0.858 - 1.717: 8 1.717 - 2.575: 0 2.575 - 3.434: 3 3.434 - 4.292: 1 Chirality restraints: 1829 Sorted by residual: chirality pdb=" CA ARG F1697 " pdb=" N ARG F1697 " pdb=" C ARG F1697 " pdb=" CB ARG F1697 " both_signs ideal model delta sigma weight residual False 2.51 -1.78 4.29 2.00e-01 2.50e+01 4.61e+02 chirality pdb=" CA ILE F1155 " pdb=" N ILE F1155 " pdb=" C ILE F1155 " pdb=" CB ILE F1155 " both_signs ideal model delta sigma weight residual False 2.43 -0.52 2.95 2.00e-01 2.50e+01 2.18e+02 chirality pdb=" CA TYR F 305 " pdb=" N TYR F 305 " pdb=" C TYR F 305 " pdb=" CB TYR F 305 " both_signs ideal model delta sigma weight residual False 2.51 -0.40 2.91 2.00e-01 2.50e+01 2.12e+02 ... (remaining 1826 not shown) Planarity restraints: 2193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F1521 " -0.179 2.00e-02 2.50e+03 2.65e-01 7.02e+02 pdb=" C ARG F1521 " 0.443 2.00e-02 2.50e+03 pdb=" O ARG F1521 " -0.227 2.00e-02 2.50e+03 pdb=" N TYR F1522 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F1744 " -0.305 2.00e-02 2.50e+03 1.57e-01 4.90e+02 pdb=" CG TYR F1744 " 0.117 2.00e-02 2.50e+03 pdb=" CD1 TYR F1744 " 0.156 2.00e-02 2.50e+03 pdb=" CD2 TYR F1744 " 0.135 2.00e-02 2.50e+03 pdb=" CE1 TYR F1744 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR F1744 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR F1744 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR F1744 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 146 " -0.111 2.00e-02 2.50e+03 1.89e-01 3.56e+02 pdb=" C SER F 146 " 0.326 2.00e-02 2.50e+03 pdb=" O SER F 146 " -0.120 2.00e-02 2.50e+03 pdb=" N GLU F 147 " -0.095 2.00e-02 2.50e+03 ... (remaining 2190 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.59: 3 1.59 - 2.42: 65 2.42 - 3.25: 12022 3.25 - 4.07: 29186 4.07 - 4.90: 49247 Warning: very small nonbonded interaction distances. Nonbonded interactions: 90523 Sorted by model distance: nonbonded pdb=" CG ASP F 152 " pdb=" OD2 ASP F 200 " model vdw 0.766 3.270 nonbonded pdb=" OD2 ASP F 152 " pdb=" OD2 ASP F 200 " model vdw 1.024 3.040 nonbonded pdb=" OD1 ASP F 152 " pdb=" OD2 ASP F 200 " model vdw 1.257 3.040 nonbonded pdb=" CZ PHE F 149 " pdb=" CD1 LEU F 261 " model vdw 1.638 3.760 nonbonded pdb=" OD1 ASN F 295 " pdb=" ND2 ASN F 303 " model vdw 1.729 3.120 ... (remaining 90518 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=0.00 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 29.550 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5181 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 : 0.028 1.645 12526 Z= 1.946 Angle : 2.987 43.340 16887 Z= 1.949 Chirality : 0.219 4.292 1829 Planarity : 0.023 0.265 2193 Dihedral : 18.830 126.570 4720 Min Nonbonded Distance : 0.766 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 9.67 % Allowed : 16.72 % Favored : 73.61 % Rotamer: Outliers : 2.58 % Allowed : 5.69 % Favored : 91.73 % Cbeta Deviations : 3.27 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 2.75 % Twisted Proline : 13.21 % Twisted General : 9.98 % 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: -6.06 (0.15), residues: 1489 helix: -4.31 (0.12), residues: 570 sheet: -2.84 (0.47), residues: 75 loop : -4.10 (0.17), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.018 TRP F 851 HIS 0.005 0.001 HIS F1852 PHE 0.089 0.013 PHE F1648 TYR 0.305 0.023 TYR F1744 ARG 0.007 0.001 ARG F 292 Details of bonding type rmsd hydrogen bonds : bond 0.30092 ( 371) hydrogen bonds : angle 9.96829 ( 1071) covalent geometry : bond 0.02810 (12525) covalent geometry : angle 2.98681 (16887) Misc. bond : bond 0.02279 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 389 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.4478 (mtp) cc_final: 0.1996 (ttt) REVERT: F 308 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5391 (tmm160) REVERT: F 864 MET cc_start: 0.5894 (ttm) cc_final: 0.5251 (ttt) REVERT: F 977 MET cc_start: 0.6275 (ttp) cc_final: 0.5542 (ttt) REVERT: F 1097 LYS cc_start: 0.7817 (mttp) cc_final: 0.7434 (ttpt) REVERT: F 1155 ILE cc_start: 0.4104 (mt) cc_final: 0.3524 (mt) REVERT: F 1209 MET cc_start: 0.3159 (ttt) cc_final: 0.1448 (mpp) REVERT: F 1298 HIS cc_start: 0.6478 (t-90) cc_final: 0.5356 (t-90) REVERT: F 1358 TYR cc_start: 0.5015 (m-80) cc_final: 0.4762 (m-80) REVERT: F 1386 VAL cc_start: 0.2922 (OUTLIER) cc_final: 0.1579 (t) REVERT: F 1396 LYS cc_start: 0.6061 (pttp) cc_final: 0.5533 (ttpt) REVERT: F 1515 LEU cc_start: 0.8172 (mp) cc_final: 0.7848 (mm) REVERT: F 1558 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5506 (pp) REVERT: F 1633 HIS cc_start: 0.7703 (p90) cc_final: 0.7336 (p90) REVERT: F 1688 ARG cc_start: 0.6523 (mtm180) cc_final: 0.5681 (mtp180) REVERT: F 1847 VAL cc_start: 0.6863 (t) cc_final: 0.6632 (t) outliers start: 34 outliers final: 9 residues processed: 417 average time/residue: 0.3691 time to fit residues: 209.5615 Evaluate side-chains 245 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 233 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 285 ASN F 679 ASN F 725 GLN F 839 GLN F 989 GLN F1001 GLN F1007 HIS F1083 ASN F1163 ASN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1232 ASN ** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1369 ASN ** F1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1632 HIS ** F1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.171750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.156272 restraints weight = 42295.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.158615 restraints weight = 28163.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.160545 restraints weight = 20603.421| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12526 Z= 0.256 Angle : 1.220 13.243 16887 Z= 0.638 Chirality : 0.091 2.443 1829 Planarity : 0.008 0.108 2193 Dihedral : 13.201 84.784 1674 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 3.02 % Allowed : 16.43 % Favored : 80.55 % Rotamer: Outliers : 0.30 % Allowed : 5.24 % Favored : 94.46 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.03 % Twisted Proline : 9.43 % Twisted General : 4.40 % 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: -4.69 (0.18), residues: 1491 helix: -2.10 (0.18), residues: 594 sheet: -2.09 (0.58), residues: 52 loop : -4.17 (0.17), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 255 HIS 0.016 0.002 HIS F1118 PHE 0.026 0.003 PHE F 924 TYR 0.025 0.003 TYR F1149 ARG 0.016 0.001 ARG F 193 Details of bonding type rmsd hydrogen bonds : bond 0.05790 ( 371) hydrogen bonds : angle 5.97317 ( 1071) covalent geometry : bond 0.00468 (12525) covalent geometry : angle 1.22029 (16887) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 298 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.3469 (mtp) cc_final: 0.2368 (ttt) REVERT: F 27 MET cc_start: 0.4958 (mmt) cc_final: 0.4686 (mmt) REVERT: F 96 LEU cc_start: 0.8532 (tp) cc_final: 0.8208 (tp) REVERT: F 158 MET cc_start: 0.7523 (tpp) cc_final: 0.7120 (ptp) REVERT: F 726 MET cc_start: 0.4066 (ttp) cc_final: 0.3529 (mtp) REVERT: F 1129 GLU cc_start: 0.4988 (mp0) cc_final: 0.4568 (tm-30) REVERT: F 1146 LEU cc_start: 0.8328 (mt) cc_final: 0.8024 (tp) REVERT: F 1157 SER cc_start: 0.9020 (p) cc_final: 0.8471 (t) REVERT: F 1181 LEU cc_start: 0.7753 (mp) cc_final: 0.7448 (tt) REVERT: F 1209 MET cc_start: 0.1623 (ttt) cc_final: 0.0836 (mpp) REVERT: F 1260 TYR cc_start: 0.6418 (m-80) cc_final: 0.6187 (m-10) REVERT: F 1298 HIS cc_start: 0.7797 (t-90) cc_final: 0.7000 (t70) REVERT: F 1396 LYS cc_start: 0.6802 (pttp) cc_final: 0.6186 (ttpt) REVERT: F 1491 MET cc_start: 0.5375 (mmp) cc_final: 0.4775 (mmp) REVERT: F 1499 PHE cc_start: 0.7555 (m-80) cc_final: 0.6785 (t80) REVERT: F 1502 GLU cc_start: 0.4896 (mt-10) cc_final: 0.4341 (tp30) REVERT: F 1510 TYR cc_start: 0.7554 (t80) cc_final: 0.7340 (t80) REVERT: F 1704 HIS cc_start: 0.8288 (m90) cc_final: 0.7958 (m90) REVERT: F 1847 VAL cc_start: 0.8911 (t) cc_final: 0.8598 (p) outliers start: 4 outliers final: 1 residues processed: 299 average time/residue: 0.3104 time to fit residues: 125.8879 Evaluate side-chains 208 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 6.9990 chunk 62 optimal weight: 0.0470 chunk 15 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 303 ASN F 675 ASN F 678 ASN F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN F1118 HIS F1122 GLN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1219 HIS ** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1339 GLN ** F1369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1626 GLN ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1751 HIS F1754 ASN F1780 ASN ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.170534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.155788 restraints weight = 42789.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.158048 restraints weight = 28303.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.159878 restraints weight = 20547.263| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12526 Z= 0.200 Angle : 1.093 13.755 16887 Z= 0.567 Chirality : 0.063 1.084 1829 Planarity : 0.007 0.095 2193 Dihedral : 11.341 72.980 1674 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 2.62 % Allowed : 17.84 % Favored : 79.54 % Rotamer: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 2.89 % 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: -4.03 (0.19), residues: 1491 helix: -1.22 (0.20), residues: 597 sheet: -1.70 (0.54), residues: 85 loop : -4.16 (0.18), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 851 HIS 0.010 0.002 HIS F1633 PHE 0.037 0.003 PHE F1468 TYR 0.035 0.003 TYR F 828 ARG 0.016 0.001 ARG F 193 Details of bonding type rmsd hydrogen bonds : bond 0.04995 ( 371) hydrogen bonds : angle 5.38859 ( 1071) covalent geometry : bond 0.00416 (12525) covalent geometry : angle 1.09344 (16887) Misc. bond : bond 0.00121 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 1.533 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: F 1 MET cc_start: 0.3648 (mtp) cc_final: 0.2791 (ttt) REVERT: F 27 MET cc_start: 0.4882 (mmt) cc_final: 0.4620 (mmp) REVERT: F 58 GLU cc_start: 0.7509 (tt0) cc_final: 0.6996 (tt0) REVERT: F 62 ARG cc_start: 0.6803 (tpp-160) cc_final: 0.6219 (tpt170) REVERT: F 139 MET cc_start: 0.1272 (pmm) cc_final: 0.0710 (pmm) REVERT: F 187 MET cc_start: 0.7190 (mmp) cc_final: 0.6055 (ttm) REVERT: F 215 MET cc_start: 0.7772 (mmp) cc_final: 0.7379 (mmm) REVERT: F 723 HIS cc_start: 0.7109 (m-70) cc_final: 0.6878 (m-70) REVERT: F 724 LYS cc_start: 0.8571 (ptpt) cc_final: 0.7849 (pttt) REVERT: F 726 MET cc_start: 0.4230 (ttp) cc_final: 0.3815 (mtp) REVERT: F 1146 LEU cc_start: 0.8737 (mt) cc_final: 0.8131 (tt) REVERT: F 1157 SER cc_start: 0.8704 (p) cc_final: 0.8332 (t) REVERT: F 1209 MET cc_start: 0.1863 (ttt) cc_final: 0.1210 (mpp) REVERT: F 1298 HIS cc_start: 0.8067 (t-90) cc_final: 0.6773 (t70) REVERT: F 1384 MET cc_start: 0.8291 (mtp) cc_final: 0.7697 (mtp) REVERT: F 1412 MET cc_start: 0.8248 (tpp) cc_final: 0.7983 (ttp) REVERT: F 1510 TYR cc_start: 0.7959 (t80) cc_final: 0.7422 (t80) REVERT: F 1519 GLU cc_start: 0.6849 (mp0) cc_final: 0.6493 (mm-30) REVERT: F 1622 LEU cc_start: 0.8852 (tp) cc_final: 0.8617 (tp) REVERT: F 1704 HIS cc_start: 0.8142 (m90) cc_final: 0.7933 (m90) REVERT: F 1849 ASP cc_start: 0.7973 (t0) cc_final: 0.7622 (m-30) outliers start: 2 outliers final: 0 residues processed: 267 average time/residue: 0.2951 time to fit residues: 108.8192 Evaluate side-chains 193 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 20 optimal weight: 0.0060 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 678 ASN F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN F1024 ASN ** F1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1163 ASN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.173167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.161834 restraints weight = 47021.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.163098 restraints weight = 35024.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.164473 restraints weight = 28098.994| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12526 Z= 0.166 Angle : 1.010 12.610 16887 Z= 0.523 Chirality : 0.056 0.823 1829 Planarity : 0.006 0.091 2193 Dihedral : 10.284 66.535 1674 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 2.08 % Allowed : 16.03 % Favored : 81.89 % Rotamer: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.51 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 2.20 % 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: -3.60 (0.20), residues: 1491 helix: -0.66 (0.20), residues: 605 sheet: -1.32 (0.61), residues: 70 loop : -4.11 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 851 HIS 0.009 0.001 HIS F1643 PHE 0.024 0.002 PHE F1468 TYR 0.027 0.002 TYR F 828 ARG 0.019 0.001 ARG F1201 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 371) hydrogen bonds : angle 4.97664 ( 1071) covalent geometry : bond 0.00338 (12525) covalent geometry : angle 1.01032 (16887) Misc. bond : bond 0.00221 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.5528 (mtp) cc_final: 0.4215 (ttt) REVERT: F 27 MET cc_start: 0.4549 (mmt) cc_final: 0.4179 (mmp) REVERT: F 58 GLU cc_start: 0.7335 (tt0) cc_final: 0.6515 (tt0) REVERT: F 187 MET cc_start: 0.7041 (mmp) cc_final: 0.6588 (ttm) REVERT: F 724 LYS cc_start: 0.8452 (ptpt) cc_final: 0.7822 (pttp) REVERT: F 726 MET cc_start: 0.4061 (ttp) cc_final: 0.3533 (mtp) REVERT: F 859 LYS cc_start: 0.8210 (mttt) cc_final: 0.7932 (mttt) REVERT: F 1146 LEU cc_start: 0.8274 (mt) cc_final: 0.7986 (tt) REVERT: F 1157 SER cc_start: 0.8109 (p) cc_final: 0.7408 (t) REVERT: F 1298 HIS cc_start: 0.7538 (t-90) cc_final: 0.6148 (t70) REVERT: F 1323 MET cc_start: 0.6469 (ptm) cc_final: 0.6001 (ppp) REVERT: F 1353 PHE cc_start: 0.4742 (m-80) cc_final: 0.4075 (m-10) REVERT: F 1384 MET cc_start: 0.8446 (mtp) cc_final: 0.7890 (mtp) REVERT: F 1412 MET cc_start: 0.7957 (tpp) cc_final: 0.7604 (ttp) REVERT: F 1510 TYR cc_start: 0.7423 (t80) cc_final: 0.7184 (t80) REVERT: F 1519 GLU cc_start: 0.5973 (mp0) cc_final: 0.5724 (mm-30) REVERT: F 1704 HIS cc_start: 0.7758 (m90) cc_final: 0.7545 (m90) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.2978 time to fit residues: 105.1160 Evaluate side-chains 192 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 140 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 0.0670 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 288 HIS F 725 GLN F 839 GLN F1001 GLN F1017 HIS ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1478 HIS F1683 ASN ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.173773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.162836 restraints weight = 47668.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.164246 restraints weight = 35710.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.165639 restraints weight = 27617.331| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.7005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12526 Z= 0.158 Angle : 0.975 12.760 16887 Z= 0.501 Chirality : 0.053 0.813 1829 Planarity : 0.006 0.092 2193 Dihedral : 9.470 61.004 1674 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 2.01 % Allowed : 16.43 % Favored : 81.56 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.51 % 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: -3.36 (0.20), residues: 1491 helix: -0.40 (0.21), residues: 615 sheet: -0.94 (0.59), residues: 83 loop : -4.14 (0.18), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 851 HIS 0.012 0.001 HIS F1643 PHE 0.026 0.002 PHE F1837 TYR 0.024 0.002 TYR F 828 ARG 0.007 0.001 ARG F 62 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 371) hydrogen bonds : angle 4.73578 ( 1071) covalent geometry : bond 0.00326 (12525) covalent geometry : angle 0.97517 (16887) Misc. bond : bond 0.00104 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 2.402 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: F 1 MET cc_start: 0.5886 (mtp) cc_final: 0.4176 (ttt) REVERT: F 27 MET cc_start: 0.4778 (mmt) cc_final: 0.4389 (mmp) REVERT: F 58 GLU cc_start: 0.7499 (tt0) cc_final: 0.6964 (tt0) REVERT: F 78 HIS cc_start: 0.6072 (t-90) cc_final: 0.5851 (t-90) REVERT: F 207 GLU cc_start: 0.8104 (pm20) cc_final: 0.7824 (pm20) REVERT: F 215 MET cc_start: 0.7012 (mmm) cc_final: 0.6606 (mmm) REVERT: F 724 LYS cc_start: 0.8557 (ptpt) cc_final: 0.7831 (pttm) REVERT: F 726 MET cc_start: 0.4011 (ttp) cc_final: 0.3412 (mtp) REVERT: F 864 MET cc_start: 0.6969 (ttm) cc_final: 0.6287 (ttm) REVERT: F 883 MET cc_start: 0.8540 (tpp) cc_final: 0.7906 (tpp) REVERT: F 937 ASP cc_start: 0.6544 (t0) cc_final: 0.5719 (t0) REVERT: F 1146 LEU cc_start: 0.8397 (mt) cc_final: 0.8119 (tt) REVERT: F 1157 SER cc_start: 0.7372 (p) cc_final: 0.6984 (t) REVERT: F 1262 ARG cc_start: 0.5704 (mmm-85) cc_final: 0.5304 (mmm160) REVERT: F 1323 MET cc_start: 0.6648 (ptm) cc_final: 0.6174 (ppp) REVERT: F 1353 PHE cc_start: 0.3734 (m-80) cc_final: 0.3217 (m-10) REVERT: F 1384 MET cc_start: 0.8357 (mtp) cc_final: 0.7768 (mtp) REVERT: F 1412 MET cc_start: 0.7999 (tpp) cc_final: 0.7657 (ttp) REVERT: F 1614 GLU cc_start: 0.7838 (tt0) cc_final: 0.7551 (tt0) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3805 time to fit residues: 134.4993 Evaluate side-chains 195 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 86 optimal weight: 30.0000 chunk 82 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 218 ASN F 286 ASN F 288 HIS F 694 GLN F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN F1024 ASN F1118 HIS ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1772 ASN ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.174650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.162774 restraints weight = 48096.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.164338 restraints weight = 34420.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.165456 restraints weight = 26486.266| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12526 Z= 0.153 Angle : 0.951 13.636 16887 Z= 0.487 Chirality : 0.052 0.810 1829 Planarity : 0.006 0.139 2193 Dihedral : 8.975 57.874 1674 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 1.88 % Allowed : 16.16 % Favored : 81.96 % Rotamer: Outliers : 0.08 % Allowed : 2.81 % Favored : 97.12 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.10 % 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: -3.19 (0.20), residues: 1491 helix: -0.15 (0.21), residues: 617 sheet: -0.51 (0.63), residues: 75 loop : -4.18 (0.17), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 851 HIS 0.010 0.001 HIS F1643 PHE 0.019 0.002 PHE F1468 TYR 0.022 0.002 TYR F1104 ARG 0.013 0.001 ARG F 291 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 371) hydrogen bonds : angle 4.61238 ( 1071) covalent geometry : bond 0.00313 (12525) covalent geometry : angle 0.95058 (16887) Misc. bond : bond 0.00154 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 1.545 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: F 1 MET cc_start: 0.5900 (mtp) cc_final: 0.4093 (tmm) REVERT: F 58 GLU cc_start: 0.7624 (tt0) cc_final: 0.7079 (tt0) REVERT: F 78 HIS cc_start: 0.6495 (t-90) cc_final: 0.6115 (t-90) REVERT: F 207 GLU cc_start: 0.8357 (pm20) cc_final: 0.8004 (pm20) REVERT: F 215 MET cc_start: 0.7144 (mmm) cc_final: 0.6766 (mmm) REVERT: F 724 LYS cc_start: 0.8546 (ptpt) cc_final: 0.7844 (pttm) REVERT: F 726 MET cc_start: 0.3775 (ttp) cc_final: 0.3197 (mtp) REVERT: F 864 MET cc_start: 0.6970 (ttm) cc_final: 0.6124 (ttm) REVERT: F 1146 LEU cc_start: 0.8680 (mt) cc_final: 0.8188 (tt) REVERT: F 1209 MET cc_start: -0.0249 (mpp) cc_final: -0.0947 (mpp) REVERT: F 1323 MET cc_start: 0.7057 (ptm) cc_final: 0.6442 (ppp) REVERT: F 1384 MET cc_start: 0.8551 (mtp) cc_final: 0.7990 (mtp) REVERT: F 1396 LYS cc_start: 0.6487 (tttt) cc_final: 0.6248 (tptm) REVERT: F 1412 MET cc_start: 0.7726 (tpp) cc_final: 0.7482 (ttp) REVERT: F 1472 ARG cc_start: 0.7306 (tmm-80) cc_final: 0.6899 (ptm-80) REVERT: F 1473 GLN cc_start: 0.4453 (tp-100) cc_final: 0.3307 (tp-100) REVERT: F 1486 LEU cc_start: 0.7783 (pp) cc_final: 0.7188 (tt) REVERT: F 1719 MET cc_start: 0.7602 (tmm) cc_final: 0.7306 (tmm) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.3438 time to fit residues: 116.8014 Evaluate side-chains 189 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 1 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 111 optimal weight: 40.0000 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 HIS F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 965 ASN F1001 GLN ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1481 ASN ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.172668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.160710 restraints weight = 47301.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.162230 restraints weight = 34236.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.163335 restraints weight = 26632.941| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.7627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12526 Z= 0.161 Angle : 0.949 12.927 16887 Z= 0.484 Chirality : 0.051 0.807 1829 Planarity : 0.006 0.101 2193 Dihedral : 8.814 56.161 1674 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 1.68 % Allowed : 16.97 % Favored : 81.35 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.17 % 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: -3.07 (0.21), residues: 1491 helix: 0.03 (0.21), residues: 621 sheet: -0.79 (0.69), residues: 61 loop : -4.10 (0.18), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 851 HIS 0.007 0.001 HIS F1751 PHE 0.023 0.002 PHE F1499 TYR 0.019 0.002 TYR F1104 ARG 0.007 0.001 ARG F1651 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 371) hydrogen bonds : angle 4.68176 ( 1071) covalent geometry : bond 0.00344 (12525) covalent geometry : angle 0.94907 (16887) Misc. bond : bond 0.00124 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.531 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: F 1 MET cc_start: 0.5989 (mtp) cc_final: 0.4117 (tmm) REVERT: F 58 GLU cc_start: 0.7379 (tt0) cc_final: 0.6652 (tt0) REVERT: F 207 GLU cc_start: 0.8374 (pm20) cc_final: 0.8134 (pm20) REVERT: F 215 MET cc_start: 0.6981 (mmm) cc_final: 0.6582 (mmm) REVERT: F 724 LYS cc_start: 0.8622 (ptpt) cc_final: 0.7966 (pttm) REVERT: F 726 MET cc_start: 0.3947 (ttp) cc_final: 0.3368 (mtp) REVERT: F 831 LEU cc_start: 0.5767 (mm) cc_final: 0.5384 (mm) REVERT: F 864 MET cc_start: 0.6976 (ttm) cc_final: 0.6070 (ttm) REVERT: F 1062 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7951 (mmtm) REVERT: F 1124 LEU cc_start: 0.6819 (mt) cc_final: 0.5960 (mt) REVERT: F 1146 LEU cc_start: 0.8752 (mt) cc_final: 0.8269 (tt) REVERT: F 1323 MET cc_start: 0.7030 (ptm) cc_final: 0.6414 (ppp) REVERT: F 1384 MET cc_start: 0.8565 (mtp) cc_final: 0.8028 (mtp) REVERT: F 1396 LYS cc_start: 0.6394 (tttt) cc_final: 0.5902 (tptm) REVERT: F 1472 ARG cc_start: 0.6782 (tmm-80) cc_final: 0.6498 (ptm-80) REVERT: F 1723 MET cc_start: 0.6834 (mmt) cc_final: 0.6366 (mmt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3392 time to fit residues: 113.3630 Evaluate side-chains 184 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 18 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 43 optimal weight: 0.1980 chunk 88 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 HIS F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 839 GLN F1001 GLN ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1852 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.173630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.162465 restraints weight = 47816.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.164052 restraints weight = 34487.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.165241 restraints weight = 25824.403| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.7800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12526 Z= 0.152 Angle : 0.932 12.523 16887 Z= 0.477 Chirality : 0.051 0.814 1829 Planarity : 0.006 0.090 2193 Dihedral : 8.542 55.917 1674 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 1.61 % Allowed : 16.23 % Favored : 82.16 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 0.83 % 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: -2.95 (0.21), residues: 1491 helix: 0.12 (0.21), residues: 613 sheet: -0.59 (0.63), residues: 76 loop : -4.07 (0.18), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 851 HIS 0.009 0.001 HIS F 78 PHE 0.019 0.002 PHE F1775 TYR 0.020 0.002 TYR F1744 ARG 0.012 0.001 ARG F1201 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 371) hydrogen bonds : angle 4.60845 ( 1071) covalent geometry : bond 0.00318 (12525) covalent geometry : angle 0.93195 (16887) Misc. bond : bond 0.00098 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.6058 (mtp) cc_final: 0.4328 (tmm) REVERT: F 58 GLU cc_start: 0.7458 (tt0) cc_final: 0.6835 (tt0) REVERT: F 207 GLU cc_start: 0.8369 (pm20) cc_final: 0.8144 (pm20) REVERT: F 215 MET cc_start: 0.7061 (mmm) cc_final: 0.6663 (mmm) REVERT: F 724 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8062 (pttm) REVERT: F 1124 LEU cc_start: 0.6631 (mt) cc_final: 0.5783 (mt) REVERT: F 1146 LEU cc_start: 0.8734 (mt) cc_final: 0.8311 (tt) REVERT: F 1323 MET cc_start: 0.6987 (ptm) cc_final: 0.6369 (ppp) REVERT: F 1384 MET cc_start: 0.8654 (mtp) cc_final: 0.8119 (mtp) REVERT: F 1412 MET cc_start: 0.8216 (tpp) cc_final: 0.7558 (ttp) REVERT: F 1418 MET cc_start: 0.6698 (tmm) cc_final: 0.6395 (tmm) REVERT: F 1704 HIS cc_start: 0.8047 (m90) cc_final: 0.7819 (m90) REVERT: F 1723 MET cc_start: 0.6838 (mmt) cc_final: 0.6389 (mmt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2773 time to fit residues: 89.8758 Evaluate side-chains 179 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 694 GLN F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.174149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.162871 restraints weight = 47253.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.164202 restraints weight = 35467.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.165058 restraints weight = 28703.875| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.8035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12526 Z= 0.159 Angle : 0.960 16.765 16887 Z= 0.487 Chirality : 0.052 0.794 1829 Planarity : 0.006 0.088 2193 Dihedral : 8.413 55.596 1674 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 1.54 % Allowed : 16.63 % Favored : 81.82 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 7.55 % Twisted General : 0.83 % 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: -2.97 (0.21), residues: 1491 helix: 0.09 (0.21), residues: 614 sheet: -0.47 (0.72), residues: 59 loop : -4.01 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 851 HIS 0.009 0.001 HIS F1643 PHE 0.018 0.002 PHE F1827 TYR 0.020 0.002 TYR F 964 ARG 0.015 0.001 ARG F1201 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 371) hydrogen bonds : angle 4.64393 ( 1071) covalent geometry : bond 0.00334 (12525) covalent geometry : angle 0.95961 (16887) Misc. bond : bond 0.00194 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.6161 (mtp) cc_final: 0.4415 (tmm) REVERT: F 147 GLU cc_start: 0.8437 (tp30) cc_final: 0.7890 (tm-30) REVERT: F 215 MET cc_start: 0.7044 (mmm) cc_final: 0.6642 (mmm) REVERT: F 724 LYS cc_start: 0.8558 (ptpt) cc_final: 0.8041 (pttm) REVERT: F 830 MET cc_start: 0.7431 (pmm) cc_final: 0.7205 (pmm) REVERT: F 1146 LEU cc_start: 0.8645 (mt) cc_final: 0.8281 (tt) REVERT: F 1323 MET cc_start: 0.6916 (ptm) cc_final: 0.6324 (ppp) REVERT: F 1374 ASP cc_start: 0.6065 (t70) cc_final: 0.5849 (m-30) REVERT: F 1384 MET cc_start: 0.8617 (mtp) cc_final: 0.8050 (mtp) REVERT: F 1412 MET cc_start: 0.8201 (tpp) cc_final: 0.7457 (ttp) REVERT: F 1581 GLU cc_start: 0.6029 (tt0) cc_final: 0.5814 (tp30) REVERT: F 1610 MET cc_start: 0.7370 (mtm) cc_final: 0.7079 (mtm) REVERT: F 1704 HIS cc_start: 0.8037 (m90) cc_final: 0.7789 (m90) REVERT: F 1723 MET cc_start: 0.6820 (mmt) cc_final: 0.6346 (mmt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2707 time to fit residues: 87.3692 Evaluate side-chains 179 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 chunk 144 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1190 GLN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.172021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.160679 restraints weight = 47286.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.161945 restraints weight = 34834.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.163504 restraints weight = 28951.697| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.8181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12526 Z= 0.165 Angle : 0.953 14.172 16887 Z= 0.485 Chirality : 0.052 0.854 1829 Planarity : 0.006 0.088 2193 Dihedral : 8.377 55.726 1674 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 1.48 % Allowed : 17.10 % Favored : 81.42 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 7.55 % Twisted General : 0.89 % 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: -3.02 (0.21), residues: 1491 helix: 0.04 (0.21), residues: 623 sheet: -0.67 (0.64), residues: 74 loop : -4.11 (0.18), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F1028 HIS 0.009 0.001 HIS F1643 PHE 0.018 0.002 PHE F1827 TYR 0.022 0.002 TYR F 244 ARG 0.018 0.001 ARG F1201 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 371) hydrogen bonds : angle 4.75334 ( 1071) covalent geometry : bond 0.00354 (12525) covalent geometry : angle 0.95325 (16887) Misc. bond : bond 0.00057 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.6587 (mtp) cc_final: 0.5049 (tmm) REVERT: F 147 GLU cc_start: 0.8364 (tp30) cc_final: 0.7719 (tm-30) REVERT: F 215 MET cc_start: 0.7096 (mmm) cc_final: 0.6663 (mmm) REVERT: F 724 LYS cc_start: 0.8419 (ptpt) cc_final: 0.7890 (pttm) REVERT: F 726 MET cc_start: 0.5107 (ttp) cc_final: 0.4671 (mtp) REVERT: F 1146 LEU cc_start: 0.8738 (mt) cc_final: 0.8340 (tt) REVERT: F 1149 TYR cc_start: 0.6447 (t80) cc_final: 0.6181 (t80) REVERT: F 1323 MET cc_start: 0.7144 (ptm) cc_final: 0.6329 (ppp) REVERT: F 1374 ASP cc_start: 0.6121 (t70) cc_final: 0.5628 (m-30) REVERT: F 1384 MET cc_start: 0.8649 (mtp) cc_final: 0.8067 (mtp) REVERT: F 1545 ARG cc_start: 0.7675 (mpt180) cc_final: 0.7334 (mpt180) REVERT: F 1704 HIS cc_start: 0.8099 (m90) cc_final: 0.7806 (m90) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3142 time to fit residues: 99.9772 Evaluate side-chains 175 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 8.9990 chunk 147 optimal weight: 0.0470 chunk 135 optimal weight: 0.0070 chunk 123 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 35 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1118 HIS ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1431 GLN ** F1808 HIS ** 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 = 0.4489 r_free = 0.4489 target = 0.174489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.163261 restraints weight = 47129.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.164571 restraints weight = 34157.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.165833 restraints weight = 28021.745| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.8388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12526 Z= 0.153 Angle : 0.951 14.422 16887 Z= 0.481 Chirality : 0.051 0.764 1829 Planarity : 0.005 0.087 2193 Dihedral : 8.157 54.869 1674 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 1.61 % Allowed : 16.70 % Favored : 81.69 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 7.55 % Twisted General : 0.62 % 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: -2.95 (0.21), residues: 1491 helix: 0.08 (0.21), residues: 616 sheet: -0.50 (0.65), residues: 72 loop : -4.04 (0.18), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F1028 HIS 0.011 0.001 HIS F1643 PHE 0.018 0.001 PHE F1827 TYR 0.017 0.002 TYR F1744 ARG 0.013 0.001 ARG F1201 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 371) hydrogen bonds : angle 4.63664 ( 1071) covalent geometry : bond 0.00317 (12525) covalent geometry : angle 0.95100 (16887) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4599.75 seconds wall clock time: 82 minutes 33.92 seconds (4953.92 seconds total)