Starting phenix.real_space_refine on Fri Mar 6 08:31:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k19_22622/03_2026/7k19_22622.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k19_22622/03_2026/7k19_22622.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 { model { file = "/net/cci-nas-00/data/ceres_data/7k19_22622/03_2026/7k19_22622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k19_22622/03_2026/7k19_22622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k19_22622/03_2026/7k19_22622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k19_22622/03_2026/7k19_22622.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 185 5.16 5 C 18559 2.51 5 N 4956 2.21 5 O 5412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29158 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 28180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3569, 28180 Classifications: {'peptide': 3569} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 1, 'PTRANS': 147, 'TRANS': 3420} Chain breaks: 20 Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 561 Unresolved non-hydrogen dihedrals: 407 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 5, 'GLU:plan': 39, 'ASP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 4, 'TYR:plan': 3, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 315 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 6.88, per 1000 atoms: 0.24 Number of scatterers: 29158 At special positions: 0 Unit cell: (129.92, 148.48, 186.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 185 16.00 P 46 15.00 O 5412 8.00 N 4956 7.00 C 18559 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: 2.37 Conformation dependent library (CDL) restraints added in 1.4 seconds 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6850 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 5 sheets defined 66.5% alpha, 0.8% beta 22 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.127A pdb=" N SER A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 40 removed outlier: 3.611A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 78 through 96 removed outlier: 3.724A pdb=" N ARG A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 Processing helix chain 'A' and resid 124 through 138 removed outlier: 4.072A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.906A pdb=" N TYR A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 removed outlier: 3.534A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 removed outlier: 4.074A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 307 through 330 removed outlier: 3.859A pdb=" N LYS A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.741A pdb=" N ARG A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.860A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 removed outlier: 3.798A pdb=" N PHE A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.827A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 477 through 491 removed outlier: 4.118A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 removed outlier: 4.240A pdb=" N SER A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 576 removed outlier: 4.041A pdb=" N VAL A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 632 removed outlier: 3.994A pdb=" N LEU A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 628 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 660 removed outlier: 3.795A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 701 through 718 removed outlier: 4.088A pdb=" N LYS A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 734 Processing helix chain 'A' and resid 744 through 747 Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.532A pdb=" N LEU A 752 " --> pdb=" O TYR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 780 removed outlier: 4.427A pdb=" N LEU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 799 removed outlier: 4.082A pdb=" N CYS A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 798 " --> pdb=" O CYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 910 through 918 removed outlier: 4.469A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 946 removed outlier: 4.104A pdb=" N VAL A 928 " --> pdb=" O ARG A 924 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.102A pdb=" N LYS A 963 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 4.775A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1003 through 1018 removed outlier: 3.788A pdb=" N VAL A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1044 removed outlier: 3.672A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A1044 " --> pdb=" O SER A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1073 through 1084 removed outlier: 3.947A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1114 Processing helix chain 'A' and resid 1123 through 1142 removed outlier: 3.952A pdb=" N ASP A1129 " --> pdb=" O GLN A1125 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A1136 " --> pdb=" O ASP A1132 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1165 through 1175 Processing helix chain 'A' and resid 1176 through 1178 No H-bonds generated for 'chain 'A' and resid 1176 through 1178' Processing helix chain 'A' and resid 1180 through 1195 removed outlier: 4.535A pdb=" N HIS A1185 " --> pdb=" O THR A1181 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1216 removed outlier: 3.826A pdb=" N LEU A1208 " --> pdb=" O PRO A1204 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1226 removed outlier: 4.049A pdb=" N GLY A1226 " --> pdb=" O ASN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1245 removed outlier: 3.577A pdb=" N ARG A1245 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1266 removed outlier: 3.504A pdb=" N LEU A1254 " --> pdb=" O LEU A1250 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A1255 " --> pdb=" O GLN A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1273 Processing helix chain 'A' and resid 1278 through 1283 removed outlier: 4.025A pdb=" N LEU A1282 " --> pdb=" O ALA A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1300 Processing helix chain 'A' and resid 1326 through 1350 removed outlier: 4.001A pdb=" N TYR A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1353 No H-bonds generated for 'chain 'A' and resid 1351 through 1353' Processing helix chain 'A' and resid 1354 through 1359 Processing helix chain 'A' and resid 1367 through 1377 removed outlier: 4.828A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1406 Proline residue: A1396 - end of helix removed outlier: 4.292A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1420 Processing helix chain 'A' and resid 1424 through 1431 Processing helix chain 'A' and resid 1444 through 1461 Processing helix chain 'A' and resid 1477 through 1492 removed outlier: 3.849A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1519 removed outlier: 3.901A pdb=" N ALA A1511 " --> pdb=" O CYS A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1533 removed outlier: 4.071A pdb=" N LEU A1533 " --> pdb=" O VAL A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1564 removed outlier: 4.275A pdb=" N SER A1561 " --> pdb=" O GLU A1557 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1562 " --> pdb=" O TYR A1558 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A1564 " --> pdb=" O TYR A1560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1557 through 1564' Processing helix chain 'A' and resid 1565 through 1574 removed outlier: 3.597A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1584 Processing helix chain 'A' and resid 1589 through 1607 removed outlier: 3.510A pdb=" N VAL A1593 " --> pdb=" O ASN A1589 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1624 removed outlier: 3.650A pdb=" N GLN A1624 " --> pdb=" O THR A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1630 removed outlier: 3.626A pdb=" N LYS A1628 " --> pdb=" O HIS A1625 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP A1630 " --> pdb=" O LYS A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1655 removed outlier: 3.622A pdb=" N ALA A1644 " --> pdb=" O GLU A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1679 removed outlier: 4.316A pdb=" N LEU A1679 " --> pdb=" O TYR A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1688 No H-bonds generated for 'chain 'A' and resid 1686 through 1688' Processing helix chain 'A' and resid 1689 through 1694 Processing helix chain 'A' and resid 1695 through 1700 removed outlier: 3.871A pdb=" N PHE A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1722 Processing helix chain 'A' and resid 1733 through 1751 Processing helix chain 'A' and resid 1757 through 1767 removed outlier: 4.068A pdb=" N VAL A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A1767 " --> pdb=" O THR A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1786 Processing helix chain 'A' and resid 1790 through 1807 Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 3.585A pdb=" N ARG A1816 " --> pdb=" O LEU A1812 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1830 Processing helix chain 'A' and resid 1837 through 1843 Processing helix chain 'A' and resid 1843 through 1852 removed outlier: 6.412A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1882 removed outlier: 4.191A pdb=" N THR A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1891 Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1910 through 1922 removed outlier: 3.536A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1955 removed outlier: 3.649A pdb=" N LEU A1939 " --> pdb=" O GLU A1935 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1974 removed outlier: 3.722A pdb=" N LYS A1973 " --> pdb=" O LYS A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1982 removed outlier: 3.510A pdb=" N LEU A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2035 through 2045 removed outlier: 3.980A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2087 through 2091 Processing helix chain 'A' and resid 2093 through 2107 removed outlier: 3.642A pdb=" N LEU A2097 " --> pdb=" O CYS A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2126 through 2135 Processing helix chain 'A' and resid 2139 through 2151 removed outlier: 4.141A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A2148 " --> pdb=" O LEU A2144 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A2149 " --> pdb=" O PHE A2145 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A2150 " --> pdb=" O LEU A2146 " (cutoff:3.500A) Processing helix chain 'A' and resid 2157 through 2161 removed outlier: 4.251A pdb=" N ALA A2161 " --> pdb=" O ARG A2158 " (cutoff:3.500A) Processing helix chain 'A' and resid 2162 through 2164 No H-bonds generated for 'chain 'A' and resid 2162 through 2164' Processing helix chain 'A' and resid 2165 through 2174 removed outlier: 3.926A pdb=" N SER A2174 " --> pdb=" O GLN A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2182 through 2196 removed outlier: 3.602A pdb=" N TRP A2196 " --> pdb=" O THR A2192 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2246 removed outlier: 3.558A pdb=" N PHE A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS A2246 " --> pdb=" O VAL A2242 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2270 through 2282 Processing helix chain 'A' and resid 2295 through 2309 Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.030A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2354 removed outlier: 3.942A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2371 Processing helix chain 'A' and resid 2378 through 2385 Processing helix chain 'A' and resid 2391 through 2402 removed outlier: 4.046A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2425 removed outlier: 3.587A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2419 through 2425' Processing helix chain 'A' and resid 2428 through 2442 removed outlier: 3.687A pdb=" N LEU A2436 " --> pdb=" O GLN A2432 " (cutoff:3.500A) Processing helix chain 'A' and resid 2443 through 2446 Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 3.819A pdb=" N ARG A2452 " --> pdb=" O PRO A2448 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2466 through 2481 removed outlier: 3.628A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A2477 " --> pdb=" O MET A2473 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A2478 " --> pdb=" O TYR A2474 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2509 removed outlier: 4.093A pdb=" N VAL A2505 " --> pdb=" O LEU A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2516 through 2526 Processing helix chain 'A' and resid 2536 through 2545 removed outlier: 3.832A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2553 through 2565 removed outlier: 4.344A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2790 through 2799 removed outlier: 3.929A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2819 removed outlier: 3.730A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 Processing helix chain 'A' and resid 2851 through 2862 Processing helix chain 'A' and resid 2863 through 2865 No H-bonds generated for 'chain 'A' and resid 2863 through 2865' Processing helix chain 'A' and resid 2875 through 2883 removed outlier: 4.228A pdb=" N ALA A2882 " --> pdb=" O ALA A2878 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 4.014A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG A2891 " --> pdb=" O PRO A2887 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2931 Processing helix chain 'A' and resid 2935 through 2941 Processing helix chain 'A' and resid 2952 through 2958 Processing helix chain 'A' and resid 2966 through 2977 removed outlier: 3.628A pdb=" N TYR A2972 " --> pdb=" O ALA A2968 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP A2973 " --> pdb=" O ALA A2969 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU A2974 " --> pdb=" O LYS A2970 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) Processing helix chain 'A' and resid 2990 through 3004 removed outlier: 3.746A pdb=" N GLU A2995 " --> pdb=" O LYS A2991 " (cutoff:3.500A) Processing helix chain 'A' and resid 3011 through 3017 Processing helix chain 'A' and resid 3027 through 3032 removed outlier: 3.650A pdb=" N TRP A3031 " --> pdb=" O LEU A3027 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3039 removed outlier: 3.605A pdb=" N THR A3039 " --> pdb=" O PHE A3035 " (cutoff:3.500A) Processing helix chain 'A' and resid 3039 through 3053 removed outlier: 4.031A pdb=" N TYR A3043 " --> pdb=" O THR A3039 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3069 Processing helix chain 'A' and resid 3083 through 3093 Processing helix chain 'A' and resid 3095 through 3117 removed outlier: 4.261A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A3117 " --> pdb=" O ASN A3113 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3146 Processing helix chain 'A' and resid 3154 through 3167 Processing helix chain 'A' and resid 3175 through 3197 Processing helix chain 'A' and resid 3227 through 3249 Processing helix chain 'A' and resid 3251 through 3262 Processing helix chain 'A' and resid 3264 through 3268 removed outlier: 3.600A pdb=" N THR A3268 " --> pdb=" O GLU A3265 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3290 removed outlier: 3.849A pdb=" N SER A3290 " --> pdb=" O CYS A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3294 through 3309 removed outlier: 3.921A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR A3303 " --> pdb=" O THR A3299 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3341 removed outlier: 3.738A pdb=" N PHE A3323 " --> pdb=" O ASN A3319 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A3341 " --> pdb=" O ILE A3337 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3360 Processing helix chain 'A' and resid 3373 through 3391 removed outlier: 4.417A pdb=" N ALA A3388 " --> pdb=" O HIS A3384 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A3389 " --> pdb=" O LEU A3385 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3428 removed outlier: 3.671A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.879A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3461 through 3464 Processing helix chain 'A' and resid 3465 through 3475 removed outlier: 3.741A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3479 through 3488 removed outlier: 4.019A pdb=" N MET A3483 " --> pdb=" O THR A3479 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3504 removed outlier: 3.715A pdb=" N MET A3502 " --> pdb=" O TRP A3498 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3525 Processing helix chain 'A' and resid 3526 through 3528 No H-bonds generated for 'chain 'A' and resid 3526 through 3528' Processing helix chain 'A' and resid 3529 through 3537 removed outlier: 3.633A pdb=" N PHE A3533 " --> pdb=" O ILE A3529 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3562 removed outlier: 4.417A pdb=" N LYS A3550 " --> pdb=" O SER A3546 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A3551 " --> pdb=" O THR A3547 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A3552 " --> pdb=" O GLY A3548 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3577 Processing helix chain 'A' and resid 3580 through 3597 removed outlier: 3.662A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU A3595 " --> pdb=" O ASP A3591 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A3597 " --> pdb=" O ARG A3593 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 3.633A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) Processing helix chain 'A' and resid 3621 through 3627 Processing helix chain 'A' and resid 3632 through 3640 removed outlier: 4.292A pdb=" N LYS A3638 " --> pdb=" O GLN A3634 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3651 removed outlier: 4.014A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A3647 " --> pdb=" O HIS A3643 " (cutoff:3.500A) Processing helix chain 'A' and resid 3660 through 3671 Processing helix chain 'A' and resid 3686 through 3690 removed outlier: 3.950A pdb=" N ASP A3689 " --> pdb=" O TRP A3686 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A3690 " --> pdb=" O MET A3687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3686 through 3690' Processing helix chain 'A' and resid 3760 through 3775 Processing helix chain 'A' and resid 3779 through 3785 removed outlier: 4.286A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 3.975A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 3.538A pdb=" N LYS A3825 " --> pdb=" O SER A3821 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A3826 " --> pdb=" O GLN A3822 " (cutoff:3.500A) Processing helix chain 'A' and resid 3836 through 3846 Processing helix chain 'A' and resid 3853 through 3859 removed outlier: 4.189A pdb=" N TYR A3859 " --> pdb=" O TYR A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 3.981A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A3874 " --> pdb=" O SER A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3891 removed outlier: 3.939A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3895 through 3915 removed outlier: 4.527A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3927 Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 4.086A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3979 through 3992 Processing helix chain 'A' and resid 3996 through 4007 Processing helix chain 'A' and resid 4013 through 4023 removed outlier: 3.873A pdb=" N LYS A4023 " --> pdb=" O LYS A4019 " (cutoff:3.500A) Processing helix chain 'A' and resid 4040 through 4052 Processing helix chain 'A' and resid 4055 through 4066 removed outlier: 3.871A pdb=" N THR A4060 " --> pdb=" O PRO A4056 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.721A pdb=" N THR A4112 " --> pdb=" O MET A4108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 3719 through 3721 removed outlier: 4.308A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 3.802A pdb=" N LYS A3753 " --> pdb=" O GLY A3801 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3809 through 3811 1427 hydrogen bonds defined for protein. 4212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 9.89 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8109 1.33 - 1.46: 6601 1.46 - 1.58: 14750 1.58 - 1.70: 91 1.70 - 1.83: 286 Bond restraints: 29837 Sorted by residual: bond pdb=" C LEU A 911 " pdb=" N PRO A 912 " ideal model delta sigma weight residual 1.334 1.364 -0.030 8.40e-03 1.42e+04 1.30e+01 bond pdb=" N VAL A1021 " pdb=" CA VAL A1021 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 8.97e+00 bond pdb=" N VAL A1992 " pdb=" CA VAL A1992 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.08e+00 bond pdb=" N THR A 398 " pdb=" CA THR A 398 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.44e+00 bond pdb=" C ASP A2289 " pdb=" N PRO A2290 " ideal model delta sigma weight residual 1.339 1.429 -0.090 3.40e-02 8.65e+02 7.03e+00 ... (remaining 29832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.97: 40397 5.97 - 11.94: 162 11.94 - 17.90: 7 17.90 - 23.87: 0 23.87 - 29.84: 2 Bond angle restraints: 40568 Sorted by residual: angle pdb=" N ASN A3311 " pdb=" CA ASN A3311 " pdb=" C ASN A3311 " ideal model delta sigma weight residual 112.03 82.19 29.84 1.31e+00 5.83e-01 5.19e+02 angle pdb=" N PRO A1469 " pdb=" CA PRO A1469 " pdb=" C PRO A1469 " ideal model delta sigma weight residual 112.47 88.12 24.35 2.06e+00 2.36e-01 1.40e+02 angle pdb=" N VAL A4033 " pdb=" CA VAL A4033 " pdb=" C VAL A4033 " ideal model delta sigma weight residual 113.20 105.88 7.32 9.60e-01 1.09e+00 5.81e+01 angle pdb=" C ASP A1019 " pdb=" N PRO A1020 " pdb=" CA PRO A1020 " ideal model delta sigma weight residual 119.84 129.10 -9.26 1.25e+00 6.40e-01 5.48e+01 angle pdb=" C LEU A1468 " pdb=" N PRO A1469 " pdb=" CA PRO A1469 " ideal model delta sigma weight residual 119.84 128.53 -8.69 1.25e+00 6.40e-01 4.84e+01 ... (remaining 40563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 15246 17.69 - 35.37: 2112 35.37 - 53.05: 520 53.05 - 70.74: 123 70.74 - 88.42: 32 Dihedral angle restraints: 18033 sinusoidal: 7530 harmonic: 10503 Sorted by residual: dihedral pdb=" N ASN A3311 " pdb=" C ASN A3311 " pdb=" CA ASN A3311 " pdb=" CB ASN A3311 " ideal model delta harmonic sigma weight residual 122.80 106.80 16.00 0 2.50e+00 1.60e-01 4.10e+01 dihedral pdb=" CA VAL A3692 " pdb=" C VAL A3692 " pdb=" N GLU A3693 " pdb=" CA GLU A3693 " ideal model delta harmonic sigma weight residual -180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA PRO A2548 " pdb=" C PRO A2548 " pdb=" N LYS A2549 " pdb=" CA LYS A2549 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 18030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 4462 0.121 - 0.241: 193 0.241 - 0.362: 8 0.362 - 0.483: 1 0.483 - 0.603: 1 Chirality restraints: 4665 Sorted by residual: chirality pdb=" CA ASN A3311 " pdb=" N ASN A3311 " pdb=" C ASN A3311 " pdb=" CB ASN A3311 " both_signs ideal model delta sigma weight residual False 2.51 3.11 -0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" CA PRO A1469 " pdb=" N PRO A1469 " pdb=" C PRO A1469 " pdb=" CB PRO A1469 " both_signs ideal model delta sigma weight residual False 2.72 3.09 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE A 740 " pdb=" CA ILE A 740 " pdb=" CG1 ILE A 740 " pdb=" CG2 ILE A 740 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4662 not shown) Planarity restraints: 4970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A1991 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C PRO A1991 " -0.085 2.00e-02 2.50e+03 pdb=" O PRO A1991 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL A1992 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1686 " 0.023 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" C LEU A1686 " -0.083 2.00e-02 2.50e+03 pdb=" O LEU A1686 " 0.033 2.00e-02 2.50e+03 pdb=" N HIS A1687 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A2182 " -0.022 2.00e-02 2.50e+03 4.54e-02 2.07e+01 pdb=" C ILE A2182 " 0.079 2.00e-02 2.50e+03 pdb=" O ILE A2182 " -0.031 2.00e-02 2.50e+03 pdb=" N HIS A2183 " -0.026 2.00e-02 2.50e+03 ... (remaining 4967 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 405 2.61 - 3.18: 25069 3.18 - 3.76: 47217 3.76 - 4.33: 59365 4.33 - 4.90: 92489 Nonbonded interactions: 224545 Sorted by model distance: nonbonded pdb=" N ASN A3311 " pdb=" N VAL A3312 " model vdw 2.038 2.560 nonbonded pdb=" O ASN A1055 " pdb=" OG SER A1058 " model vdw 2.242 3.040 nonbonded pdb=" O LYS A 205 " pdb=" OG1 THR A 209 " model vdw 2.242 3.040 nonbonded pdb=" O TYR A1560 " pdb=" OG SER A1564 " model vdw 2.251 3.040 nonbonded pdb=" O SER A 72 " pdb=" OG SER A 72 " model vdw 2.258 3.040 ... (remaining 224540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.510 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: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.006 0.090 29837 Z= 0.287 Angle : 1.100 29.841 40568 Z= 0.599 Chirality : 0.058 0.603 4665 Planarity : 0.008 0.090 4970 Dihedral : 17.644 88.425 11183 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.73 % Favored : 86.96 % Rotamer: Outliers : 0.65 % Allowed : 12.15 % Favored : 87.20 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.91 (0.11), residues: 3527 helix: -2.62 (0.08), residues: 2189 sheet: -1.86 (0.82), residues: 39 loop : -4.32 (0.14), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1340 TYR 0.026 0.002 TYR A3610 PHE 0.039 0.002 PHE A2260 TRP 0.014 0.002 TRP A3916 HIS 0.008 0.002 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00607 (29837) covalent geometry : angle 1.10040 (40568) hydrogen bonds : bond 0.12024 ( 1482) hydrogen bonds : angle 6.29283 ( 4322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 396 time to evaluate : 1.110 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: A 59 PHE cc_start: 0.4739 (m-80) cc_final: 0.4433 (m-10) REVERT: A 189 MET cc_start: 0.5052 (mpp) cc_final: 0.4776 (mpp) REVERT: A 264 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7879 (mmm160) REVERT: A 749 VAL cc_start: 0.9148 (m) cc_final: 0.8940 (t) REVERT: A 785 MET cc_start: 0.7112 (mmm) cc_final: 0.6833 (mmt) REVERT: A 1015 ASP cc_start: 0.7326 (p0) cc_final: 0.6559 (p0) REVERT: A 1392 MET cc_start: 0.7139 (tmm) cc_final: 0.6895 (tmm) REVERT: A 1804 MET cc_start: 0.9117 (ptm) cc_final: 0.8840 (tmm) REVERT: A 1860 GLU cc_start: 0.9280 (pm20) cc_final: 0.8804 (mm-30) REVERT: A 1871 MET cc_start: 0.9255 (ttm) cc_final: 0.9040 (ttm) REVERT: A 2038 GLU cc_start: 0.7336 (mp0) cc_final: 0.6994 (mp0) REVERT: A 2126 MET cc_start: 0.7480 (ttm) cc_final: 0.7109 (ttm) REVERT: A 2222 HIS cc_start: 0.8158 (m-70) cc_final: 0.7631 (m90) REVERT: A 2408 MET cc_start: 0.6941 (ttm) cc_final: 0.6517 (tpt) REVERT: A 2442 MET cc_start: 0.8980 (ptm) cc_final: 0.8696 (ptt) REVERT: A 2473 MET cc_start: 0.7543 (ttp) cc_final: 0.7188 (ttp) REVERT: A 2545 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8344 (pp) REVERT: A 3046 ARG cc_start: 0.8343 (ttt90) cc_final: 0.8068 (ptm160) REVERT: A 3256 MET cc_start: 0.7925 (tpp) cc_final: 0.7664 (tpp) REVERT: A 3523 ASP cc_start: 0.7295 (m-30) cc_final: 0.6882 (m-30) REVERT: A 3687 MET cc_start: 0.8040 (ptp) cc_final: 0.6837 (ptp) REVERT: A 3850 HIS cc_start: 0.7377 (t-170) cc_final: 0.7114 (m90) REVERT: A 3869 THR cc_start: 0.8627 (m) cc_final: 0.8349 (t) outliers start: 20 outliers final: 10 residues processed: 414 average time/residue: 0.1981 time to fit residues: 130.0835 Evaluate side-chains 283 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 233 ASN A 339 GLN A 377 ASN A 533 HIS A 739 ASN ** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS A1418 HIS A1568 ASN A1598 ASN A1603 GLN A1665 HIS A1737 ASN A1817 GLN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1897 ASN ** A2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2270 ASN A2306 ASN A2432 GLN A2481 HIS A2553 HIS A2859 GLN A2977 ASN A3028 ASN A3037 GLN A3113 ASN A3150 ASN A3154 GLN A3319 ASN A3383 GLN A3457 ASN A3510 GLN A3551 ASN A3569 GLN A3577 GLN A3679 ASN A3697 ASN A3787 GLN A3863 ASN A3927 ASN A4088 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.086145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.070347 restraints weight = 151080.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071723 restraints weight = 104028.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.072841 restraints weight = 68896.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.073006 restraints weight = 56949.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.073113 restraints weight = 48687.060| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29837 Z= 0.158 Angle : 0.728 14.094 40568 Z= 0.379 Chirality : 0.043 0.190 4665 Planarity : 0.005 0.082 4970 Dihedral : 13.305 88.272 4337 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.45 % Favored : 88.49 % Rotamer: Outliers : 0.10 % Allowed : 6.17 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.13), residues: 3527 helix: -1.35 (0.10), residues: 2235 sheet: -2.20 (0.68), residues: 58 loop : -3.95 (0.15), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3965 TYR 0.021 0.001 TYR A3168 PHE 0.028 0.002 PHE A2851 TRP 0.011 0.001 TRP A3686 HIS 0.008 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00340 (29837) covalent geometry : angle 0.72763 (40568) hydrogen bonds : bond 0.04481 ( 1482) hydrogen bonds : angle 5.02090 ( 4322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 380 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.5030 (m-80) cc_final: 0.4512 (m-10) REVERT: A 441 MET cc_start: 0.6598 (tpp) cc_final: 0.6387 (tpp) REVERT: A 682 TYR cc_start: 0.6958 (t80) cc_final: 0.6722 (t80) REVERT: A 880 MET cc_start: 0.8286 (mmm) cc_final: 0.7876 (mmm) REVERT: A 939 MET cc_start: 0.8757 (mmm) cc_final: 0.8532 (mmm) REVERT: A 940 PHE cc_start: 0.7820 (t80) cc_final: 0.7365 (t80) REVERT: A 962 TYR cc_start: 0.8105 (m-80) cc_final: 0.7628 (m-80) REVERT: A 1074 LYS cc_start: 0.8880 (tppt) cc_final: 0.8657 (tppt) REVERT: A 1109 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8267 (mt-10) REVERT: A 1348 LEU cc_start: 0.9277 (tt) cc_final: 0.8966 (mm) REVERT: A 2038 GLU cc_start: 0.7671 (mp0) cc_final: 0.7153 (mp0) REVERT: A 2126 MET cc_start: 0.7818 (ttm) cc_final: 0.7411 (ttm) REVERT: A 2379 MET cc_start: 0.8943 (mmt) cc_final: 0.8425 (mmm) REVERT: A 2408 MET cc_start: 0.6775 (ttm) cc_final: 0.6459 (tpp) REVERT: A 2442 MET cc_start: 0.8798 (ptm) cc_final: 0.8558 (ptt) REVERT: A 2445 LYS cc_start: 0.7639 (mmtt) cc_final: 0.6996 (mmtm) REVERT: A 3046 ARG cc_start: 0.8741 (ttt90) cc_final: 0.8501 (ptm160) REVERT: A 3061 LEU cc_start: 0.8782 (tp) cc_final: 0.8489 (tp) REVERT: A 3173 MET cc_start: 0.8806 (mmt) cc_final: 0.8572 (mmt) REVERT: A 3523 ASP cc_start: 0.6933 (m-30) cc_final: 0.6592 (m-30) REVERT: A 3572 ILE cc_start: 0.9318 (mm) cc_final: 0.8716 (mm) REVERT: A 3746 ARG cc_start: 0.8071 (mpp80) cc_final: 0.7506 (mpp80) REVERT: A 3850 HIS cc_start: 0.7194 (t-170) cc_final: 0.6910 (m90) outliers start: 3 outliers final: 1 residues processed: 383 average time/residue: 0.1802 time to fit residues: 113.1875 Evaluate side-chains 272 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 20 optimal weight: 0.0470 chunk 228 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 335 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 48 optimal weight: 0.0270 overall best weight: 1.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A1146 ASN A1598 ASN A1665 HIS A1830 HIS A2183 HIS A2306 ASN A2475 ASN A3524 ASN A3679 ASN A3787 GLN ** A3924 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 = 0.3738 r_free = 0.3738 target = 0.087613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.072165 restraints weight = 148909.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073422 restraints weight = 104842.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074771 restraints weight = 72297.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.074888 restraints weight = 58537.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.074984 restraints weight = 48818.543| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29837 Z= 0.128 Angle : 0.680 13.424 40568 Z= 0.350 Chirality : 0.042 0.179 4665 Planarity : 0.004 0.080 4970 Dihedral : 13.012 84.251 4337 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.46 % Favored : 89.48 % Rotamer: Outliers : 0.10 % Allowed : 4.59 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.13), residues: 3527 helix: -0.75 (0.10), residues: 2247 sheet: -2.02 (0.75), residues: 45 loop : -3.70 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1178 TYR 0.021 0.001 TYR A 366 PHE 0.033 0.001 PHE A 629 TRP 0.009 0.001 TRP A2164 HIS 0.007 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00271 (29837) covalent geometry : angle 0.67990 (40568) hydrogen bonds : bond 0.03938 ( 1482) hydrogen bonds : angle 4.67289 ( 4322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 387 time to evaluate : 1.262 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: A 59 PHE cc_start: 0.4971 (m-80) cc_final: 0.4523 (m-10) REVERT: A 529 ASP cc_start: 0.8054 (p0) cc_final: 0.7584 (t70) REVERT: A 880 MET cc_start: 0.7961 (mmm) cc_final: 0.7669 (mmm) REVERT: A 962 TYR cc_start: 0.8012 (m-80) cc_final: 0.7560 (m-80) REVERT: A 970 LEU cc_start: 0.8652 (pt) cc_final: 0.7681 (mt) REVERT: A 1348 LEU cc_start: 0.9190 (tt) cc_final: 0.8922 (mm) REVERT: A 1871 MET cc_start: 0.9263 (ttm) cc_final: 0.9023 (ttm) REVERT: A 2038 GLU cc_start: 0.7591 (mp0) cc_final: 0.7052 (mp0) REVERT: A 2126 MET cc_start: 0.7650 (ttm) cc_final: 0.7307 (ttm) REVERT: A 2307 MET cc_start: 0.8268 (tpt) cc_final: 0.7964 (tpp) REVERT: A 2379 MET cc_start: 0.8848 (mmt) cc_final: 0.8309 (mmm) REVERT: A 2445 LYS cc_start: 0.7609 (mmtt) cc_final: 0.6970 (mmtm) REVERT: A 3061 LEU cc_start: 0.8645 (tp) cc_final: 0.8344 (tp) REVERT: A 3450 MET cc_start: 0.4074 (ttt) cc_final: 0.3741 (ttt) REVERT: A 3519 GLU cc_start: 0.8535 (tp30) cc_final: 0.8282 (tp30) REVERT: A 3523 ASP cc_start: 0.7013 (m-30) cc_final: 0.6708 (m-30) REVERT: A 3572 ILE cc_start: 0.9357 (mm) cc_final: 0.9152 (mm) REVERT: A 3610 TYR cc_start: 0.6829 (t80) cc_final: 0.6498 (t80) REVERT: A 3668 LEU cc_start: 0.8878 (pp) cc_final: 0.8666 (mt) REVERT: A 3706 ASP cc_start: 0.8993 (p0) cc_final: 0.8591 (p0) REVERT: A 3746 ARG cc_start: 0.8018 (mpp80) cc_final: 0.7521 (mpp80) REVERT: A 4109 ASP cc_start: 0.6947 (t70) cc_final: 0.6743 (t0) outliers start: 3 outliers final: 2 residues processed: 389 average time/residue: 0.1781 time to fit residues: 114.7122 Evaluate side-chains 283 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 145 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 102 optimal weight: 0.0570 chunk 297 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 219 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2475 ASN ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3679 ASN ** A3927 ASN ** 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 = 0.3744 r_free = 0.3744 target = 0.087917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.072122 restraints weight = 149613.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073458 restraints weight = 104082.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.074122 restraints weight = 71235.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074488 restraints weight = 60269.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.074623 restraints weight = 52559.945| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29837 Z= 0.127 Angle : 0.670 13.643 40568 Z= 0.342 Chirality : 0.041 0.187 4665 Planarity : 0.004 0.078 4970 Dihedral : 12.888 82.621 4337 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.55 % Favored : 89.42 % Rotamer: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.14), residues: 3527 helix: -0.45 (0.11), residues: 2270 sheet: -1.44 (0.92), residues: 33 loop : -3.63 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2333 TYR 0.019 0.001 TYR A1940 PHE 0.034 0.001 PHE A3189 TRP 0.011 0.001 TRP A3842 HIS 0.007 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00274 (29837) covalent geometry : angle 0.66980 (40568) hydrogen bonds : bond 0.03721 ( 1482) hydrogen bonds : angle 4.52725 ( 4322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 1.130 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: A 59 PHE cc_start: 0.5037 (m-80) cc_final: 0.4583 (m-10) REVERT: A 529 ASP cc_start: 0.8077 (p0) cc_final: 0.7405 (t70) REVERT: A 880 MET cc_start: 0.8003 (mmm) cc_final: 0.7756 (mmm) REVERT: A 940 PHE cc_start: 0.7659 (t80) cc_final: 0.7088 (t80) REVERT: A 962 TYR cc_start: 0.8103 (m-80) cc_final: 0.7623 (m-80) REVERT: A 970 LEU cc_start: 0.8680 (pt) cc_final: 0.7706 (mt) REVERT: A 1015 ASP cc_start: 0.8131 (p0) cc_final: 0.7684 (p0) REVERT: A 1155 ARG cc_start: 0.7701 (tmt170) cc_final: 0.7206 (tmm160) REVERT: A 1348 LEU cc_start: 0.9270 (tt) cc_final: 0.8918 (mm) REVERT: A 1743 MET cc_start: 0.8653 (mmt) cc_final: 0.8175 (mmm) REVERT: A 1871 MET cc_start: 0.9280 (ttm) cc_final: 0.9043 (ttm) REVERT: A 2038 GLU cc_start: 0.7223 (mp0) cc_final: 0.6726 (mp0) REVERT: A 2040 MET cc_start: 0.7780 (tpp) cc_final: 0.7510 (tpp) REVERT: A 2379 MET cc_start: 0.8966 (mmt) cc_final: 0.8352 (mmm) REVERT: A 2445 LYS cc_start: 0.7642 (mmtt) cc_final: 0.6991 (mmtm) REVERT: A 2860 ASP cc_start: 0.8110 (m-30) cc_final: 0.7857 (m-30) REVERT: A 3046 ARG cc_start: 0.8583 (ptm160) cc_final: 0.8352 (ptm160) REVERT: A 3450 MET cc_start: 0.3975 (ttt) cc_final: 0.3589 (ttt) REVERT: A 3519 GLU cc_start: 0.8687 (tp30) cc_final: 0.8361 (tp30) REVERT: A 3523 ASP cc_start: 0.7076 (m-30) cc_final: 0.6529 (m-30) REVERT: A 3572 ILE cc_start: 0.9374 (mm) cc_final: 0.9041 (mm) REVERT: A 3668 LEU cc_start: 0.8911 (pp) cc_final: 0.8687 (mt) REVERT: A 3706 ASP cc_start: 0.8981 (p0) cc_final: 0.8392 (p0) REVERT: A 3746 ARG cc_start: 0.7964 (mpp80) cc_final: 0.7473 (mpp80) REVERT: A 3771 MET cc_start: 0.8338 (ttt) cc_final: 0.8043 (ttt) REVERT: A 4109 ASP cc_start: 0.7046 (t70) cc_final: 0.6820 (t0) outliers start: 1 outliers final: 1 residues processed: 381 average time/residue: 0.1776 time to fit residues: 111.5564 Evaluate side-chains 274 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 190 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 46 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN A1603 GLN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1957 ASN A2103 HIS ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2414 GLN A2475 ASN ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3423 GLN A3679 ASN A3908 HIS ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.086996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.070821 restraints weight = 150646.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.072178 restraints weight = 97295.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.073122 restraints weight = 70746.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.073781 restraints weight = 56132.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074257 restraints weight = 47493.998| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29837 Z= 0.149 Angle : 0.683 13.581 40568 Z= 0.350 Chirality : 0.042 0.214 4665 Planarity : 0.004 0.077 4970 Dihedral : 12.873 82.774 4337 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.06 % Favored : 88.91 % Rotamer: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.14), residues: 3527 helix: -0.33 (0.11), residues: 2273 sheet: -2.14 (0.98), residues: 28 loop : -3.51 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3125 TYR 0.018 0.001 TYR A1940 PHE 0.019 0.002 PHE A1990 TRP 0.008 0.001 TRP A3842 HIS 0.008 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00320 (29837) covalent geometry : angle 0.68255 (40568) hydrogen bonds : bond 0.03794 ( 1482) hydrogen bonds : angle 4.52817 ( 4322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 1.178 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: A 59 PHE cc_start: 0.5231 (m-80) cc_final: 0.4599 (m-10) REVERT: A 491 CYS cc_start: 0.8599 (m) cc_final: 0.8348 (m) REVERT: A 529 ASP cc_start: 0.8190 (p0) cc_final: 0.7313 (t70) REVERT: A 754 MET cc_start: 0.7747 (mtt) cc_final: 0.7427 (mtt) REVERT: A 793 LEU cc_start: 0.8956 (mt) cc_final: 0.8723 (mm) REVERT: A 880 MET cc_start: 0.8036 (mmm) cc_final: 0.7697 (mmm) REVERT: A 940 PHE cc_start: 0.7667 (t80) cc_final: 0.7068 (t80) REVERT: A 962 TYR cc_start: 0.8175 (m-80) cc_final: 0.7633 (m-80) REVERT: A 1107 TYR cc_start: 0.8050 (m-10) cc_final: 0.7503 (m-80) REVERT: A 1348 LEU cc_start: 0.9319 (tt) cc_final: 0.9030 (mm) REVERT: A 1570 GLU cc_start: 0.8131 (tp30) cc_final: 0.7827 (tt0) REVERT: A 1743 MET cc_start: 0.8700 (mmt) cc_final: 0.8182 (mmm) REVERT: A 1871 MET cc_start: 0.9267 (ttm) cc_final: 0.9023 (ttm) REVERT: A 2038 GLU cc_start: 0.7573 (mp0) cc_final: 0.7052 (mp0) REVERT: A 2379 MET cc_start: 0.9035 (mmt) cc_final: 0.8354 (mmm) REVERT: A 2445 LYS cc_start: 0.7585 (mmtt) cc_final: 0.6909 (mmtm) REVERT: A 2860 ASP cc_start: 0.8298 (m-30) cc_final: 0.8029 (m-30) REVERT: A 3046 ARG cc_start: 0.8634 (ptm160) cc_final: 0.8427 (ptm160) REVERT: A 3450 MET cc_start: 0.4027 (ttt) cc_final: 0.3660 (ttt) REVERT: A 3572 ILE cc_start: 0.9381 (mm) cc_final: 0.9018 (mm) REVERT: A 3665 MET cc_start: 0.6960 (mtt) cc_final: 0.6548 (mtt) REVERT: A 3668 LEU cc_start: 0.8905 (pp) cc_final: 0.8686 (mt) REVERT: A 3706 ASP cc_start: 0.9083 (p0) cc_final: 0.8559 (p0) REVERT: A 4109 ASP cc_start: 0.7132 (t70) cc_final: 0.6889 (t0) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 0.1787 time to fit residues: 110.5959 Evaluate side-chains 272 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 231 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 238 optimal weight: 0.2980 chunk 286 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 135 optimal weight: 0.8980 chunk 289 optimal weight: 6.9990 chunk 292 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN A1721 HIS ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2414 GLN A2475 ASN A2534 ASN A3093 GLN A3139 GLN ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3679 ASN A3808 ASN A3927 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.088337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.072584 restraints weight = 147628.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073885 restraints weight = 102660.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.075065 restraints weight = 69493.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075356 restraints weight = 55397.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075396 restraints weight = 45846.431| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29837 Z= 0.124 Angle : 0.669 13.562 40568 Z= 0.339 Chirality : 0.041 0.192 4665 Planarity : 0.004 0.077 4970 Dihedral : 12.795 83.871 4337 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.29 % Favored : 89.68 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.14), residues: 3527 helix: -0.15 (0.11), residues: 2277 sheet: -2.21 (0.84), residues: 40 loop : -3.48 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1034 TYR 0.025 0.001 TYR A 762 PHE 0.026 0.001 PHE A2851 TRP 0.032 0.001 TRP A1829 HIS 0.010 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00268 (29837) covalent geometry : angle 0.66918 (40568) hydrogen bonds : bond 0.03553 ( 1482) hydrogen bonds : angle 4.36067 ( 4322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.5133 (m-80) cc_final: 0.4549 (m-10) REVERT: A 251 PHE cc_start: 0.8571 (m-80) cc_final: 0.8365 (m-80) REVERT: A 294 PHE cc_start: 0.8660 (t80) cc_final: 0.8381 (t80) REVERT: A 491 CYS cc_start: 0.8792 (m) cc_final: 0.8494 (m) REVERT: A 529 ASP cc_start: 0.8117 (p0) cc_final: 0.7231 (t70) REVERT: A 793 LEU cc_start: 0.8996 (mt) cc_final: 0.8778 (mm) REVERT: A 880 MET cc_start: 0.8040 (mmm) cc_final: 0.7625 (mmm) REVERT: A 933 LEU cc_start: 0.8604 (pp) cc_final: 0.8050 (tp) REVERT: A 940 PHE cc_start: 0.7645 (t80) cc_final: 0.7077 (t80) REVERT: A 962 TYR cc_start: 0.8155 (m-80) cc_final: 0.7589 (m-80) REVERT: A 970 LEU cc_start: 0.8677 (pt) cc_final: 0.7664 (mt) REVERT: A 1015 ASP cc_start: 0.8202 (p0) cc_final: 0.7774 (p0) REVERT: A 1025 LEU cc_start: 0.8555 (tp) cc_final: 0.8290 (tp) REVERT: A 1107 TYR cc_start: 0.7871 (m-10) cc_final: 0.7655 (m-80) REVERT: A 1342 MET cc_start: 0.7588 (mpp) cc_final: 0.6662 (mpp) REVERT: A 1348 LEU cc_start: 0.9301 (tt) cc_final: 0.8934 (mm) REVERT: A 1570 GLU cc_start: 0.8160 (tp30) cc_final: 0.7835 (tt0) REVERT: A 1871 MET cc_start: 0.9260 (ttm) cc_final: 0.8731 (ttm) REVERT: A 2038 GLU cc_start: 0.7019 (mp0) cc_final: 0.6799 (mp0) REVERT: A 2277 LEU cc_start: 0.9483 (mt) cc_final: 0.9222 (mt) REVERT: A 2379 MET cc_start: 0.8946 (mmt) cc_final: 0.8364 (mmm) REVERT: A 2445 LYS cc_start: 0.7507 (mmtt) cc_final: 0.6917 (mmtm) REVERT: A 2860 ASP cc_start: 0.8168 (m-30) cc_final: 0.7905 (m-30) REVERT: A 3046 ARG cc_start: 0.8588 (ptm160) cc_final: 0.8320 (ptm160) REVERT: A 3090 TYR cc_start: 0.7321 (m-10) cc_final: 0.6908 (m-80) REVERT: A 3450 MET cc_start: 0.3840 (ttt) cc_final: 0.3445 (ttt) REVERT: A 3572 ILE cc_start: 0.9383 (mm) cc_final: 0.9016 (mm) REVERT: A 3665 MET cc_start: 0.6946 (mtt) cc_final: 0.6556 (mtt) REVERT: A 3668 LEU cc_start: 0.8923 (pp) cc_final: 0.8699 (mt) REVERT: A 3771 MET cc_start: 0.8250 (ttt) cc_final: 0.7963 (ttt) REVERT: A 3846 MET cc_start: 0.8656 (tpp) cc_final: 0.8406 (tpp) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.1748 time to fit residues: 115.8013 Evaluate side-chains 289 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 356 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 351 optimal weight: 0.0030 chunk 136 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 279 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 318 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 613 HIS ** A1175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2414 GLN A2475 ASN ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3516 HIS A3671 ASN A3679 ASN ** A3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3966 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.086278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.070169 restraints weight = 151329.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.071476 restraints weight = 99312.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.072369 restraints weight = 73045.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.073020 restraints weight = 58530.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073487 restraints weight = 49656.966| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29837 Z= 0.185 Angle : 0.721 14.796 40568 Z= 0.370 Chirality : 0.044 0.190 4665 Planarity : 0.004 0.075 4970 Dihedral : 12.887 83.877 4337 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.37 % Favored : 88.60 % Rotamer: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.14), residues: 3527 helix: -0.24 (0.11), residues: 2267 sheet: -1.98 (0.83), residues: 46 loop : -3.47 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3125 TYR 0.028 0.002 TYR A 762 PHE 0.021 0.002 PHE A2257 TRP 0.030 0.002 TRP A2981 HIS 0.015 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00400 (29837) covalent geometry : angle 0.72076 (40568) hydrogen bonds : bond 0.03954 ( 1482) hydrogen bonds : angle 4.61737 ( 4322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.5349 (m-80) cc_final: 0.4713 (m-10) REVERT: A 251 PHE cc_start: 0.8612 (m-80) cc_final: 0.8351 (m-80) REVERT: A 410 MET cc_start: 0.8541 (tpt) cc_final: 0.7931 (tpt) REVERT: A 682 TYR cc_start: 0.7660 (t80) cc_final: 0.7440 (t80) REVERT: A 793 LEU cc_start: 0.8966 (mt) cc_final: 0.8732 (mm) REVERT: A 940 PHE cc_start: 0.7708 (t80) cc_final: 0.7108 (t80) REVERT: A 1074 LYS cc_start: 0.9013 (tptt) cc_final: 0.8795 (tppt) REVERT: A 1107 TYR cc_start: 0.8315 (m-10) cc_final: 0.7605 (m-80) REVERT: A 1155 ARG cc_start: 0.7715 (tmt170) cc_final: 0.7275 (tmm160) REVERT: A 1342 MET cc_start: 0.7686 (mpp) cc_final: 0.6748 (mpp) REVERT: A 1570 GLU cc_start: 0.8137 (tp30) cc_final: 0.7782 (tt0) REVERT: A 1742 CYS cc_start: 0.9138 (t) cc_final: 0.8863 (p) REVERT: A 1871 MET cc_start: 0.9312 (ttm) cc_final: 0.9047 (ttm) REVERT: A 2039 GLU cc_start: 0.8615 (tp30) cc_final: 0.8338 (tp30) REVERT: A 2184 TYR cc_start: 0.7839 (t80) cc_final: 0.7595 (t80) REVERT: A 2185 MET cc_start: 0.8451 (mmm) cc_final: 0.7619 (mmm) REVERT: A 2307 MET cc_start: 0.8424 (tpp) cc_final: 0.8141 (tpp) REVERT: A 2379 MET cc_start: 0.9017 (mmt) cc_final: 0.8415 (mmm) REVERT: A 2445 LYS cc_start: 0.7552 (mmtt) cc_final: 0.6857 (mmtm) REVERT: A 2860 ASP cc_start: 0.8413 (m-30) cc_final: 0.8159 (m-30) REVERT: A 3046 ARG cc_start: 0.8636 (ptm160) cc_final: 0.8395 (ptm160) REVERT: A 3089 LEU cc_start: 0.8866 (pp) cc_final: 0.8649 (pp) REVERT: A 3090 TYR cc_start: 0.7643 (m-10) cc_final: 0.7139 (m-80) REVERT: A 3176 MET cc_start: 0.8658 (mmp) cc_final: 0.8332 (mmt) REVERT: A 3450 MET cc_start: 0.3937 (ttt) cc_final: 0.3548 (ttt) REVERT: A 3572 ILE cc_start: 0.9390 (mm) cc_final: 0.9177 (mm) REVERT: A 3665 MET cc_start: 0.6978 (mtt) cc_final: 0.6579 (mtt) REVERT: A 3668 LEU cc_start: 0.8960 (pp) cc_final: 0.8737 (mt) REVERT: A 3846 MET cc_start: 0.8726 (tpp) cc_final: 0.8248 (tpp) REVERT: A 4109 ASP cc_start: 0.7225 (t70) cc_final: 0.6949 (t0) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1724 time to fit residues: 106.6920 Evaluate side-chains 268 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 304 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 327 optimal weight: 0.2980 chunk 309 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN A1830 HIS ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2475 ASN A2483 ASN ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3679 ASN A3808 ASN A3924 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.088813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.072601 restraints weight = 147124.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.073945 restraints weight = 96933.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074888 restraints weight = 71215.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075560 restraints weight = 56544.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.076020 restraints weight = 47822.624| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29837 Z= 0.120 Angle : 0.679 14.456 40568 Z= 0.340 Chirality : 0.042 0.190 4665 Planarity : 0.004 0.076 4970 Dihedral : 12.776 84.162 4337 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.04 % Favored : 89.93 % Rotamer: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3527 helix: -0.00 (0.11), residues: 2274 sheet: -1.19 (1.05), residues: 34 loop : -3.34 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 406 TYR 0.028 0.001 TYR A1874 PHE 0.034 0.001 PHE A 396 TRP 0.042 0.001 TRP A2479 HIS 0.007 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00259 (29837) covalent geometry : angle 0.67942 (40568) hydrogen bonds : bond 0.03402 ( 1482) hydrogen bonds : angle 4.30530 ( 4322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 1.186 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: A 59 PHE cc_start: 0.5185 (m-80) cc_final: 0.4636 (m-10) REVERT: A 251 PHE cc_start: 0.8470 (m-80) cc_final: 0.8190 (m-80) REVERT: A 529 ASP cc_start: 0.8087 (p0) cc_final: 0.7443 (t70) REVERT: A 723 ASP cc_start: 0.6945 (p0) cc_final: 0.6718 (p0) REVERT: A 933 LEU cc_start: 0.8702 (pp) cc_final: 0.8216 (tp) REVERT: A 940 PHE cc_start: 0.7663 (t80) cc_final: 0.7069 (t80) REVERT: A 962 TYR cc_start: 0.8169 (m-80) cc_final: 0.7592 (m-80) REVERT: A 970 LEU cc_start: 0.8653 (pt) cc_final: 0.7673 (mt) REVERT: A 1025 LEU cc_start: 0.8435 (tp) cc_final: 0.8147 (tp) REVERT: A 1107 TYR cc_start: 0.8203 (m-10) cc_final: 0.7668 (m-80) REVERT: A 1342 MET cc_start: 0.7767 (mpp) cc_final: 0.7452 (mtm) REVERT: A 1348 LEU cc_start: 0.9299 (pp) cc_final: 0.8683 (mp) REVERT: A 1369 MET cc_start: 0.7911 (mpp) cc_final: 0.7677 (mpp) REVERT: A 2039 GLU cc_start: 0.8574 (tp30) cc_final: 0.8085 (pt0) REVERT: A 2184 TYR cc_start: 0.7612 (t80) cc_final: 0.7340 (t80) REVERT: A 2185 MET cc_start: 0.8345 (mmm) cc_final: 0.7638 (mmm) REVERT: A 2277 LEU cc_start: 0.9457 (mt) cc_final: 0.9216 (mt) REVERT: A 2379 MET cc_start: 0.8871 (mmt) cc_final: 0.8306 (mmm) REVERT: A 2445 LYS cc_start: 0.7624 (mmtt) cc_final: 0.7050 (mmtm) REVERT: A 2816 ILE cc_start: 0.9175 (mm) cc_final: 0.8942 (mm) REVERT: A 2860 ASP cc_start: 0.8129 (m-30) cc_final: 0.7908 (m-30) REVERT: A 3046 ARG cc_start: 0.8556 (ptm160) cc_final: 0.8328 (ptm160) REVERT: A 3450 MET cc_start: 0.3777 (ttt) cc_final: 0.3408 (ttt) REVERT: A 3665 MET cc_start: 0.6897 (mtt) cc_final: 0.6490 (mtt) REVERT: A 3668 LEU cc_start: 0.8946 (pp) cc_final: 0.8727 (mt) REVERT: A 3687 MET cc_start: 0.8694 (pmm) cc_final: 0.8442 (pmm) REVERT: A 3710 LYS cc_start: 0.8620 (mppt) cc_final: 0.8033 (tppt) REVERT: A 3771 MET cc_start: 0.8252 (ttt) cc_final: 0.7793 (ttt) REVERT: A 3846 MET cc_start: 0.8622 (tpp) cc_final: 0.8184 (tpp) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.1721 time to fit residues: 113.4441 Evaluate side-chains 291 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 77 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 324 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 353 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN A1624 GLN ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2414 GLN ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3808 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.088588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072246 restraints weight = 147159.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073631 restraints weight = 94913.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.074601 restraints weight = 69159.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075286 restraints weight = 54597.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.075730 restraints weight = 46137.898| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29837 Z= 0.124 Angle : 0.679 13.642 40568 Z= 0.342 Chirality : 0.042 0.195 4665 Planarity : 0.004 0.075 4970 Dihedral : 12.732 83.110 4337 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.15 % Favored : 89.82 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3527 helix: 0.05 (0.11), residues: 2279 sheet: -1.13 (1.05), residues: 34 loop : -3.33 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2232 TYR 0.025 0.001 TYR A1874 PHE 0.029 0.001 PHE A2851 TRP 0.034 0.002 TRP A2981 HIS 0.010 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00274 (29837) covalent geometry : angle 0.67894 (40568) hydrogen bonds : bond 0.03397 ( 1482) hydrogen bonds : angle 4.32319 ( 4322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.5190 (m-80) cc_final: 0.4679 (m-10) REVERT: A 251 PHE cc_start: 0.8436 (m-80) cc_final: 0.8171 (m-80) REVERT: A 529 ASP cc_start: 0.8232 (p0) cc_final: 0.7489 (t70) REVERT: A 933 LEU cc_start: 0.8753 (pp) cc_final: 0.8279 (tp) REVERT: A 940 PHE cc_start: 0.7658 (t80) cc_final: 0.7048 (t80) REVERT: A 962 TYR cc_start: 0.8216 (m-80) cc_final: 0.7595 (m-80) REVERT: A 970 LEU cc_start: 0.8720 (pt) cc_final: 0.7738 (mt) REVERT: A 1025 LEU cc_start: 0.8572 (tp) cc_final: 0.8301 (tp) REVERT: A 1107 TYR cc_start: 0.8180 (m-10) cc_final: 0.7696 (m-80) REVERT: A 1342 MET cc_start: 0.7908 (mpp) cc_final: 0.6795 (mpp) REVERT: A 1348 LEU cc_start: 0.9247 (pp) cc_final: 0.8659 (mp) REVERT: A 1369 MET cc_start: 0.8003 (mpp) cc_final: 0.7710 (mpp) REVERT: A 1774 MET cc_start: 0.7841 (mtm) cc_final: 0.7414 (mmm) REVERT: A 1871 MET cc_start: 0.9246 (ttm) cc_final: 0.8953 (ttm) REVERT: A 2039 GLU cc_start: 0.8594 (tp30) cc_final: 0.8089 (pt0) REVERT: A 2184 TYR cc_start: 0.7659 (t80) cc_final: 0.7367 (t80) REVERT: A 2185 MET cc_start: 0.8453 (mmm) cc_final: 0.7721 (mmm) REVERT: A 2277 LEU cc_start: 0.9447 (mt) cc_final: 0.9131 (mt) REVERT: A 2307 MET cc_start: 0.8727 (tpp) cc_final: 0.8195 (tpp) REVERT: A 2379 MET cc_start: 0.8921 (mmt) cc_final: 0.8261 (mmm) REVERT: A 2445 LYS cc_start: 0.7623 (mmtt) cc_final: 0.6973 (mmtm) REVERT: A 2860 ASP cc_start: 0.8196 (m-30) cc_final: 0.7964 (m-30) REVERT: A 3028 ASN cc_start: 0.8673 (t0) cc_final: 0.8351 (t0) REVERT: A 3046 ARG cc_start: 0.8619 (ptm160) cc_final: 0.8418 (ptm160) REVERT: A 3450 MET cc_start: 0.3737 (ttt) cc_final: 0.3395 (ttt) REVERT: A 3483 MET cc_start: 0.8921 (ppp) cc_final: 0.8406 (ppp) REVERT: A 3572 ILE cc_start: 0.9373 (mm) cc_final: 0.9162 (mm) REVERT: A 3665 MET cc_start: 0.6902 (mtt) cc_final: 0.6497 (mtt) REVERT: A 3668 LEU cc_start: 0.8942 (pp) cc_final: 0.8730 (mt) REVERT: A 3723 ASP cc_start: 0.8868 (t0) cc_final: 0.8635 (p0) REVERT: A 3746 ARG cc_start: 0.7942 (mpp80) cc_final: 0.7308 (mpp80) REVERT: A 3846 MET cc_start: 0.8595 (tpp) cc_final: 0.8299 (tpp) REVERT: A 4109 ASP cc_start: 0.7077 (t70) cc_final: 0.6834 (t0) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.1724 time to fit residues: 112.6278 Evaluate side-chains 283 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 104 optimal weight: 0.0970 chunk 22 optimal weight: 0.5980 chunk 243 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2414 GLN ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3679 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.087515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.071354 restraints weight = 149612.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.072642 restraints weight = 99250.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073535 restraints weight = 73655.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074197 restraints weight = 59145.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074659 restraints weight = 50194.433| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29837 Z= 0.152 Angle : 0.709 13.629 40568 Z= 0.358 Chirality : 0.043 0.197 4665 Planarity : 0.004 0.075 4970 Dihedral : 12.774 82.916 4337 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.63 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.14), residues: 3527 helix: 0.01 (0.11), residues: 2274 sheet: -1.36 (1.01), residues: 34 loop : -3.29 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 746 TYR 0.026 0.001 TYR A1874 PHE 0.023 0.001 PHE A3571 TRP 0.041 0.002 TRP A2479 HIS 0.015 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00337 (29837) covalent geometry : angle 0.70908 (40568) hydrogen bonds : bond 0.03621 ( 1482) hydrogen bonds : angle 4.42593 ( 4322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.5355 (m-80) cc_final: 0.4836 (m-10) REVERT: A 251 PHE cc_start: 0.8464 (m-80) cc_final: 0.8203 (m-80) REVERT: A 933 LEU cc_start: 0.8764 (pp) cc_final: 0.8286 (tp) REVERT: A 962 TYR cc_start: 0.8098 (m-80) cc_final: 0.7532 (m-80) REVERT: A 1107 TYR cc_start: 0.8188 (m-10) cc_final: 0.7757 (m-80) REVERT: A 1348 LEU cc_start: 0.9249 (pp) cc_final: 0.8661 (mp) REVERT: A 1750 LEU cc_start: 0.9204 (tt) cc_final: 0.8968 (tt) REVERT: A 1762 MET cc_start: 0.9253 (ttt) cc_final: 0.9030 (ttm) REVERT: A 1871 MET cc_start: 0.9260 (ttm) cc_final: 0.8955 (ttm) REVERT: A 2039 GLU cc_start: 0.8538 (tp30) cc_final: 0.8158 (pt0) REVERT: A 2184 TYR cc_start: 0.7660 (t80) cc_final: 0.7354 (t80) REVERT: A 2185 MET cc_start: 0.8450 (mmm) cc_final: 0.7721 (mmm) REVERT: A 2277 LEU cc_start: 0.9499 (mt) cc_final: 0.9178 (mt) REVERT: A 2307 MET cc_start: 0.8755 (tpp) cc_final: 0.8175 (tpp) REVERT: A 2379 MET cc_start: 0.8945 (mmt) cc_final: 0.8288 (mmm) REVERT: A 2445 LYS cc_start: 0.7679 (mmtt) cc_final: 0.6963 (mmtm) REVERT: A 2860 ASP cc_start: 0.8300 (m-30) cc_final: 0.8080 (m-30) REVERT: A 3028 ASN cc_start: 0.8676 (t0) cc_final: 0.8404 (t0) REVERT: A 3483 MET cc_start: 0.8921 (ppp) cc_final: 0.8405 (ppp) REVERT: A 3710 LYS cc_start: 0.8709 (mppt) cc_final: 0.8118 (tppt) REVERT: A 3746 ARG cc_start: 0.7960 (mpp80) cc_final: 0.7322 (mpp80) REVERT: A 3846 MET cc_start: 0.8653 (tpp) cc_final: 0.8307 (tpp) REVERT: A 3858 MET cc_start: 0.6460 (mtt) cc_final: 0.6235 (mtt) REVERT: A 4109 ASP cc_start: 0.7182 (t70) cc_final: 0.6911 (t0) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1641 time to fit residues: 100.6270 Evaluate side-chains 267 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 229 optimal weight: 0.8980 chunk 288 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A 738 HIS A1175 HIS ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2414 GLN A2475 ASN ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3679 ASN A3808 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.087056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.070886 restraints weight = 150774.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.072169 restraints weight = 99799.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.073085 restraints weight = 73914.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.073743 restraints weight = 59019.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074190 restraints weight = 50150.058| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29837 Z= 0.159 Angle : 0.715 13.860 40568 Z= 0.362 Chirality : 0.043 0.199 4665 Planarity : 0.004 0.076 4970 Dihedral : 12.802 83.382 4337 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.69 % Favored : 89.28 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.14), residues: 3527 helix: -0.04 (0.11), residues: 2274 sheet: -1.84 (0.82), residues: 46 loop : -3.31 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1822 TYR 0.026 0.002 TYR A 762 PHE 0.023 0.001 PHE A3571 TRP 0.051 0.002 TRP A2981 HIS 0.012 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00352 (29837) covalent geometry : angle 0.71523 (40568) hydrogen bonds : bond 0.03728 ( 1482) hydrogen bonds : angle 4.48642 ( 4322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4539.94 seconds wall clock time: 79 minutes 47.48 seconds (4787.48 seconds total)