Starting phenix.real_space_refine on Thu Sep 26 06:49:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/09_2024/7ask_11895.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/09_2024/7ask_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/09_2024/7ask_11895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/09_2024/7ask_11895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/09_2024/7ask_11895.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/09_2024/7ask_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-5461/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: 7.44, per 1000 atoms: 0.61 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=0, symmetry=0 Time building additional restraints: 2.68 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: 1.33 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: 3.85 Time building geometry restraints manager: 3.21 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: 4 1.59 - 2.42: 65 2.42 - 3.25: 12024 3.25 - 4.07: 29186 4.07 - 4.90: 49247 Warning: very small nonbonded interaction distances. Nonbonded interactions: 90526 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=" CD2 LEU F 261 " pdb=" ND2 ASN F 295 " model vdw 1.407 3.540 nonbonded pdb=" CZ PHE F 149 " pdb=" CD1 LEU F 261 " model vdw 1.638 3.760 ... (remaining 90521 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.620 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- 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 12525 Z= 1.721 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 : 16.79 % Favored : 73.54 % 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 *********************** 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 fitting. rotamer outliers: 34 poor density : 389 time to evaluate : 1.319 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: 0.4478 (mtp) cc_final: 0.1993 (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: 0.5249 (ttt) REVERT: F 977 MET cc_start: 0.6275 (ttp) cc_final: 0.5544 (ttt) REVERT: F 1097 LYS cc_start: 0.7817 (mttp) cc_final: 0.7436 (ttpt) REVERT: F 1155 ILE cc_start: 0.4104 (mt) cc_final: 0.3548 (mt) REVERT: F 1209 MET cc_start: 0.3159 (ttt) cc_final: 0.1444 (mpp) REVERT: F 1298 HIS cc_start: 0.6478 (t-90) cc_final: 0.5355 (t-90) REVERT: F 1358 TYR cc_start: 0.5015 (m-80) cc_final: 0.4766 (m-80) REVERT: F 1386 VAL cc_start: 0.2922 (OUTLIER) cc_final: 0.1570 (t) REVERT: F 1396 LYS cc_start: 0.6061 (pttp) cc_final: 0.5536 (ttpt) REVERT: F 1515 LEU cc_start: 0.8172 (mp) cc_final: 0.7851 (mm) REVERT: F 1558 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5509 (pp) REVERT: F 1633 HIS cc_start: 0.7703 (p90) cc_final: 0.7335 (p90) REVERT: F 1688 ARG cc_start: 0.6523 (mtm180) cc_final: 0.5690 (mtp180) REVERT: F 1847 VAL cc_start: 0.6863 (t) cc_final: 0.6626 (t) outliers start: 34 outliers final: 9 residues processed: 417 average time/residue: 0.3229 time to fit residues: 179.2311 Evaluate side-chains 245 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 233 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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: 6.9990 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 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 679 ASN F 725 GLN F 839 GLN F 989 GLN F1001 GLN F1007 HIS F1083 ASN ** F1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1163 ASN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5307 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12525 Z= 0.300 Angle : 1.231 13.757 16887 Z= 0.643 Chirality : 0.093 2.495 1829 Planarity : 0.008 0.102 2193 Dihedral : 13.548 86.177 1674 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 2.95 % Allowed : 17.37 % Favored : 79.68 % Rotamer: Outliers : 0.38 % Allowed : 5.01 % Favored : 94.61 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.03 % Twisted Proline : 9.43 % Twisted General : 4.68 % 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: -4.72 (0.18), residues: 1491 helix: -2.15 (0.18), residues: 585 sheet: -2.17 (0.57), residues: 52 loop : -4.16 (0.17), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 255 HIS 0.015 0.002 HIS F1118 PHE 0.033 0.003 PHE F 140 TYR 0.027 0.003 TYR F1149 ARG 0.022 0.001 ARG F 193 *********************** 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 300 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 295 time to evaluate : 1.334 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: 0.3902 (mtp) cc_final: 0.2554 (ttt) REVERT: F 96 LEU cc_start: 0.6667 (tp) cc_final: 0.6440 (tp) REVERT: F 726 MET cc_start: 0.2967 (ttp) cc_final: 0.2576 (mtp) REVERT: F 859 LYS cc_start: 0.7803 (mtmt) cc_final: 0.7433 (mtmt) REVERT: F 864 MET cc_start: 0.6419 (ttm) cc_final: 0.6151 (ttm) REVERT: F 886 GLN cc_start: 0.7945 (pt0) cc_final: 0.7630 (pt0) REVERT: F 1157 SER cc_start: 0.7508 (p) cc_final: 0.6561 (t) REVERT: F 1209 MET cc_start: 0.2827 (ttt) cc_final: 0.1931 (mpp) REVERT: F 1298 HIS cc_start: 0.6385 (t-90) cc_final: 0.5751 (t70) REVERT: F 1443 MET cc_start: 0.0711 (ppp) cc_final: 0.0441 (ptm) REVERT: F 1491 MET cc_start: 0.4217 (OUTLIER) cc_final: 0.3555 (mmp) REVERT: F 1704 HIS cc_start: 0.7376 (m90) cc_final: 0.6889 (m90) REVERT: F 1847 VAL cc_start: 0.8063 (t) cc_final: 0.7634 (p) outliers start: 5 outliers final: 1 residues processed: 296 average time/residue: 0.2917 time to fit residues: 117.0960 Evaluate side-chains 197 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 149 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 HIS ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 675 ASN F 678 ASN F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN F1118 HIS F1122 GLN ** F1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1232 ASN ** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1339 GLN F1361 HIS ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12525 Z= 0.309 Angle : 1.131 14.044 16887 Z= 0.586 Chirality : 0.064 1.072 1829 Planarity : 0.007 0.096 2193 Dihedral : 11.571 73.540 1674 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 2.75 % Allowed : 17.64 % Favored : 79.61 % Rotamer: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.07 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 3.09 % 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: -4.10 (0.19), residues: 1491 helix: -1.29 (0.20), residues: 593 sheet: -1.69 (0.54), residues: 80 loop : -4.17 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP F 851 HIS 0.009 0.002 HIS F1156 PHE 0.045 0.003 PHE F1013 TYR 0.036 0.003 TYR F 828 ARG 0.010 0.001 ARG F1476 *********************** 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 260 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 258 time to evaluate : 1.393 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: 0.3652 (mtp) cc_final: 0.2780 (ttt) REVERT: F 686 LYS cc_start: 0.5803 (tmtt) cc_final: 0.5538 (tmtt) REVERT: F 724 LYS cc_start: 0.8339 (ptpt) cc_final: 0.7708 (pttt) REVERT: F 726 MET cc_start: 0.3085 (ttp) cc_final: 0.2780 (mtp) REVERT: F 729 LEU cc_start: 0.5007 (tp) cc_final: 0.4752 (tp) REVERT: F 864 MET cc_start: 0.7272 (ttm) cc_final: 0.6459 (ttt) REVERT: F 1134 MET cc_start: 0.6234 (ttt) cc_final: 0.5864 (ttt) REVERT: F 1157 SER cc_start: 0.7353 (p) cc_final: 0.6605 (t) REVERT: F 1209 MET cc_start: 0.2618 (ttt) cc_final: 0.1999 (mpp) REVERT: F 1412 MET cc_start: 0.7424 (tpp) cc_final: 0.7221 (ttp) REVERT: F 1443 MET cc_start: 0.0757 (ppp) cc_final: 0.0529 (ptm) REVERT: F 1510 TYR cc_start: 0.7350 (t80) cc_final: 0.6805 (t80) REVERT: F 1519 GLU cc_start: 0.5074 (mp0) cc_final: 0.4798 (mm-30) REVERT: F 1643 HIS cc_start: 0.6810 (m170) cc_final: 0.6530 (m-70) REVERT: F 1704 HIS cc_start: 0.7328 (m90) cc_final: 0.6838 (m90) outliers start: 2 outliers final: 1 residues processed: 259 average time/residue: 0.2718 time to fit residues: 97.5632 Evaluate side-chains 202 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 0.2980 chunk 146 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 HIS F 303 ASN 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 F1156 HIS ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1478 HIS ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12525 Z= 0.236 Angle : 1.034 12.684 16887 Z= 0.536 Chirality : 0.057 0.889 1829 Planarity : 0.007 0.146 2193 Dihedral : 10.620 68.252 1674 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 2.21 % Allowed : 16.50 % Favored : 81.29 % Rotamer: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.89 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 2.41 % 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: -3.78 (0.20), residues: 1491 helix: -0.91 (0.20), residues: 611 sheet: -1.14 (0.66), residues: 63 loop : -4.15 (0.18), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 851 HIS 0.006 0.001 HIS F 142 PHE 0.032 0.002 PHE F1468 TYR 0.027 0.002 TYR F 828 ARG 0.017 0.001 ARG F1201 *********************** 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 244 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 1.243 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: 0.5540 (mtp) cc_final: 0.4193 (ttt) REVERT: F 291 ARG cc_start: 0.6253 (tpt90) cc_final: 0.5427 (tpm170) REVERT: F 724 LYS cc_start: 0.8127 (ptpt) cc_final: 0.7606 (pttt) REVERT: F 726 MET cc_start: 0.3129 (ttp) cc_final: 0.2757 (mtp) REVERT: F 1024 ASN cc_start: 0.8239 (m-40) cc_final: 0.7945 (t0) REVERT: F 1032 LEU cc_start: 0.7043 (tt) cc_final: 0.6471 (tt) REVERT: F 1157 SER cc_start: 0.6581 (p) cc_final: 0.5954 (t) REVERT: F 1412 MET cc_start: 0.7091 (tpp) cc_final: 0.6627 (ttp) REVERT: F 1443 MET cc_start: 0.0780 (ppp) cc_final: 0.0357 (ptt) REVERT: F 1614 GLU cc_start: 0.7373 (tt0) cc_final: 0.7056 (tt0) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.2826 time to fit residues: 96.6779 Evaluate side-chains 182 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 30.0000 chunk 60 optimal weight: 0.1980 chunk 125 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 725 GLN F 839 GLN F1001 GLN F1163 ASN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1704 HIS F1772 ASN ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1831 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5513 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12525 Z= 0.271 Angle : 1.034 12.933 16887 Z= 0.533 Chirality : 0.055 0.875 1829 Planarity : 0.007 0.102 2193 Dihedral : 10.092 65.646 1674 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 2.01 % Allowed : 17.97 % Favored : 80.01 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.72 % 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: -3.65 (0.20), residues: 1491 helix: -0.68 (0.20), residues: 600 sheet: -1.16 (0.59), residues: 80 loop : -4.19 (0.18), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 851 HIS 0.008 0.002 HIS F1633 PHE 0.029 0.002 PHE F1468 TYR 0.025 0.002 TYR F 828 ARG 0.015 0.001 ARG F1476 *********************** 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 240 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.373 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: 0.5651 (mtp) cc_final: 0.4270 (ttt) REVERT: F 187 MET cc_start: 0.5158 (mmt) cc_final: 0.4671 (mmt) REVERT: F 291 ARG cc_start: 0.5894 (tpt90) cc_final: 0.5022 (tpm170) REVERT: F 724 LYS cc_start: 0.8271 (ptpt) cc_final: 0.7774 (pttp) REVERT: F 726 MET cc_start: 0.2605 (ttp) cc_final: 0.2382 (mtp) REVERT: F 1157 SER cc_start: 0.6616 (p) cc_final: 0.6205 (t) REVERT: F 1201 ARG cc_start: 0.4973 (ppt170) cc_final: 0.4730 (tmm-80) REVERT: F 1443 MET cc_start: 0.0889 (ppp) cc_final: 0.0555 (ptt) REVERT: F 1707 PHE cc_start: 0.5582 (m-10) cc_final: 0.5349 (m-10) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2799 time to fit residues: 93.0397 Evaluate side-chains 185 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 9.9990 chunk 132 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 0.0770 chunk 77 optimal weight: 9.9990 overall best weight: 3.0262 ------------------------------------------------------------------------------- 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 956 HIS F 965 ASN F1001 GLN F1017 HIS F1024 ASN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12525 Z= 0.217 Angle : 0.988 12.549 16887 Z= 0.507 Chirality : 0.052 0.773 1829 Planarity : 0.006 0.092 2193 Dihedral : 9.624 60.625 1674 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 1.81 % Allowed : 17.24 % Favored : 80.95 % Rotamer: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.51 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.58 % 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: -3.46 (0.20), residues: 1491 helix: -0.41 (0.20), residues: 602 sheet: -1.18 (0.59), residues: 80 loop : -4.17 (0.18), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F1028 HIS 0.006 0.001 HIS F1633 PHE 0.030 0.002 PHE F1468 TYR 0.028 0.002 TYR F1510 ARG 0.011 0.001 ARG F1201 *********************** 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 250 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.504 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: 0.5808 (mtp) cc_final: 0.4334 (ttt) REVERT: F 189 CYS cc_start: 0.2517 (t) cc_final: 0.2164 (t) REVERT: F 724 LYS cc_start: 0.8051 (ptpt) cc_final: 0.7667 (pttp) REVERT: F 864 MET cc_start: 0.6433 (ttm) cc_final: 0.6128 (ttt) REVERT: F 1124 LEU cc_start: 0.5860 (mt) cc_final: 0.5347 (mt) REVERT: F 1157 SER cc_start: 0.6337 (p) cc_final: 0.6041 (t) REVERT: F 1631 MET cc_start: 0.6349 (tmm) cc_final: 0.5912 (ttp) REVERT: F 1707 PHE cc_start: 0.5533 (m-10) cc_final: 0.5205 (m-10) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.3102 time to fit residues: 107.8963 Evaluate side-chains 186 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 4.9990 chunk 16 optimal weight: 0.0050 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 123 optimal weight: 0.0470 chunk 82 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.0096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 286 ASN F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5323 moved from start: 0.7684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12525 Z= 0.201 Angle : 0.964 12.700 16887 Z= 0.494 Chirality : 0.052 0.771 1829 Planarity : 0.006 0.090 2193 Dihedral : 9.087 57.103 1674 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 1.81 % Allowed : 16.90 % Favored : 81.29 % 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 : 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: -3.25 (0.20), residues: 1491 helix: -0.15 (0.21), residues: 608 sheet: -0.94 (0.60), residues: 76 loop : -4.17 (0.18), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F1028 HIS 0.009 0.001 HIS F1751 PHE 0.028 0.002 PHE F1468 TYR 0.024 0.002 TYR F 305 ARG 0.009 0.001 ARG F1201 *********************** 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 fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.327 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: 0.5751 (mtp) cc_final: 0.4443 (ttt) REVERT: F 27 MET cc_start: 0.3605 (mmp) cc_final: 0.2745 (mmp) REVERT: F 291 ARG cc_start: 0.5880 (tpt90) cc_final: 0.5472 (tpm170) REVERT: F 724 LYS cc_start: 0.8085 (ptpt) cc_final: 0.7474 (pttt) REVERT: F 864 MET cc_start: 0.6394 (ttm) cc_final: 0.6061 (ttt) REVERT: F 877 TYR cc_start: 0.7054 (t80) cc_final: 0.6849 (t80) REVERT: F 883 MET cc_start: 0.7872 (tpp) cc_final: 0.7384 (tpp) REVERT: F 937 ASP cc_start: 0.5740 (t0) cc_final: 0.5148 (t0) REVERT: F 1124 LEU cc_start: 0.5926 (mt) cc_final: 0.5316 (mt) REVERT: F 1297 MET cc_start: 0.4749 (mmp) cc_final: 0.4537 (mmm) REVERT: F 1412 MET cc_start: 0.6801 (tpp) cc_final: 0.6243 (ttp) REVERT: F 1631 MET cc_start: 0.6141 (tmm) cc_final: 0.5894 (ttp) REVERT: F 1643 HIS cc_start: 0.5519 (m-70) cc_final: 0.5148 (m-70) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2857 time to fit residues: 94.0913 Evaluate side-chains 191 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS ** F 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1831 HIS F1852 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5500 moved from start: 0.7859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12525 Z= 0.254 Angle : 0.992 12.249 16887 Z= 0.509 Chirality : 0.052 0.810 1829 Planarity : 0.006 0.090 2193 Dihedral : 9.123 56.526 1674 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 1.61 % Allowed : 18.04 % Favored : 80.35 % Rotamer: Outliers : 0.08 % Allowed : 2.43 % Favored : 97.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.38 % 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: -3.32 (0.20), residues: 1491 helix: -0.19 (0.21), residues: 608 sheet: -1.28 (0.72), residues: 56 loop : -4.13 (0.18), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 851 HIS 0.008 0.002 HIS F1643 PHE 0.027 0.002 PHE F 157 TYR 0.036 0.002 TYR F 305 ARG 0.006 0.001 ARG F 941 *********************** 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 233 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.468 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: 0.5826 (mtp) cc_final: 0.5058 (ttt) REVERT: F 291 ARG cc_start: 0.5968 (tpt90) cc_final: 0.5647 (tpm170) REVERT: F 724 LYS cc_start: 0.8283 (ptpt) cc_final: 0.7527 (pttp) REVERT: F 877 TYR cc_start: 0.6940 (t80) cc_final: 0.6740 (t80) REVERT: F 1124 LEU cc_start: 0.5858 (mt) cc_final: 0.5198 (mt) REVERT: F 1157 SER cc_start: 0.6565 (p) cc_final: 0.6263 (t) REVERT: F 1188 THR cc_start: 0.3560 (m) cc_final: 0.3343 (t) REVERT: F 1195 LEU cc_start: 0.6320 (mm) cc_final: 0.6056 (mm) REVERT: F 1486 LEU cc_start: 0.7082 (pp) cc_final: 0.6856 (pp) REVERT: F 1631 MET cc_start: 0.6510 (tmm) cc_final: 0.6209 (ttp) outliers start: 1 outliers final: 1 residues processed: 233 average time/residue: 0.2721 time to fit residues: 88.3351 Evaluate side-chains 184 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 82 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 144 optimal weight: 0.0040 overall best weight: 1.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 696 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5373 moved from start: 0.8138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12525 Z= 0.212 Angle : 0.975 15.826 16887 Z= 0.496 Chirality : 0.051 0.742 1829 Planarity : 0.006 0.092 2193 Dihedral : 8.774 55.759 1674 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 1.61 % Allowed : 17.24 % Favored : 81.15 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.03 % 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: -3.18 (0.20), residues: 1491 helix: 0.03 (0.21), residues: 597 sheet: -1.18 (0.68), residues: 61 loop : -4.10 (0.18), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F1356 HIS 0.011 0.001 HIS F1643 PHE 0.023 0.002 PHE F 150 TYR 0.029 0.002 TYR F 296 ARG 0.009 0.001 ARG F 306 *********************** 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 236 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.340 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: 0.5771 (mtp) cc_final: 0.5021 (ttt) REVERT: F 291 ARG cc_start: 0.5836 (tpt90) cc_final: 0.4813 (tpt170) REVERT: F 724 LYS cc_start: 0.8047 (ptpt) cc_final: 0.7432 (pttp) REVERT: F 735 MET cc_start: 0.2532 (tpt) cc_final: 0.1922 (tpt) REVERT: F 883 MET cc_start: 0.7910 (tpp) cc_final: 0.7417 (tpp) REVERT: F 937 ASP cc_start: 0.5850 (t0) cc_final: 0.5304 (t0) REVERT: F 1124 LEU cc_start: 0.5887 (mt) cc_final: 0.5172 (mt) REVERT: F 1149 TYR cc_start: 0.5879 (t80) cc_final: 0.5671 (t80) REVERT: F 1374 ASP cc_start: 0.4466 (t70) cc_final: 0.4258 (p0) REVERT: F 1486 LEU cc_start: 0.6892 (pp) cc_final: 0.6659 (pp) REVERT: F 1512 VAL cc_start: 0.7930 (p) cc_final: 0.7601 (p) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2927 time to fit residues: 94.2262 Evaluate side-chains 186 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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: 4.9990 chunk 68 optimal weight: 0.0020 chunk 100 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 overall best weight: 1.5190 ------------------------------------------------------------------------------- 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** F1001 GLN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 moved from start: 0.8355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12525 Z= 0.201 Angle : 0.954 13.839 16887 Z= 0.487 Chirality : 0.050 0.740 1829 Planarity : 0.006 0.090 2193 Dihedral : 8.472 54.743 1674 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 1.61 % Allowed : 17.10 % Favored : 81.29 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 0.96 % 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: -3.12 (0.21), residues: 1491 helix: 0.07 (0.21), residues: 597 sheet: -1.28 (0.65), residues: 66 loop : -4.06 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F1028 HIS 0.013 0.001 HIS F1643 PHE 0.031 0.002 PHE F 150 TYR 0.022 0.002 TYR F 296 ARG 0.015 0.001 ARG F1197 ********************** 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 228 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.386 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: 0.5714 (mtp) cc_final: 0.5013 (ttt) REVERT: F 291 ARG cc_start: 0.5727 (tpt90) cc_final: 0.4818 (tpt170) REVERT: F 724 LYS cc_start: 0.7770 (ptpt) cc_final: 0.7311 (pttp) REVERT: F 844 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6426 (mm-30) REVERT: F 864 MET cc_start: 0.6732 (ttm) cc_final: 0.6087 (ttm) REVERT: F 937 ASP cc_start: 0.5500 (t0) cc_final: 0.5247 (t0) REVERT: F 1124 LEU cc_start: 0.5711 (mt) cc_final: 0.5008 (mt) REVERT: F 1293 LEU cc_start: 0.4642 (tt) cc_final: 0.4402 (tp) REVERT: F 1353 PHE cc_start: 0.3084 (m-10) cc_final: 0.2706 (m-10) REVERT: F 1486 LEU cc_start: 0.6907 (pp) cc_final: 0.6658 (pp) REVERT: F 1517 GLU cc_start: 0.7016 (tt0) cc_final: 0.6759 (tm-30) REVERT: F 1631 MET cc_start: 0.6148 (ttp) cc_final: 0.5848 (ttp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2753 time to fit residues: 87.6304 Evaluate side-chains 185 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 142 HIS F 675 ASN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1361 HIS ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1831 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.170940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.159474 restraints weight = 47447.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.160976 restraints weight = 34166.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.162012 restraints weight = 26460.030| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.8485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12525 Z= 0.211 Angle : 0.946 13.742 16887 Z= 0.482 Chirality : 0.051 0.741 1829 Planarity : 0.006 0.099 2193 Dihedral : 8.347 53.973 1674 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 1.54 % Allowed : 17.77 % Favored : 80.68 % Rotamer: Outliers : 0.08 % Allowed : 0.53 % Favored : 99.39 % Cbeta Deviations : 0.14 % 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: -3.06 (0.21), residues: 1491 helix: 0.16 (0.21), residues: 596 sheet: -1.26 (0.65), residues: 65 loop : -4.05 (0.18), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F1028 HIS 0.009 0.001 HIS F1643 PHE 0.027 0.002 PHE F1294 TYR 0.018 0.002 TYR F1744 ARG 0.016 0.001 ARG F1197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.82 seconds wall clock time: 53 minutes 24.41 seconds (3204.41 seconds total)