Starting phenix.real_space_refine on Fri Jul 3 20:27:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w9t_32372/07_2026/7w9t_32372.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9t_32372/07_2026/7w9t_32372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w9t_32372/07_2026/7w9t_32372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9t_32372/07_2026/7w9t_32372.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7w9t_32372/07_2026/7w9t_32372.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w9t_32372/07_2026/7w9t_32372.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w9t_32372/07_2026/7w9t_32372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9t_32372/07_2026/7w9t_32372.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.098 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 21 5.49 5 S 105 5.16 5 C 9797 2.51 5 N 2241 2.21 5 O 2677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14841 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1417, 11419 Classifications: {'peptide': 1417} Link IDs: {'PCIS': 3, 'PTRANS': 47, 'TRANS': 1366} Chain breaks: 3 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 119, 970 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 978 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 883 Unusual residues: {'9SL': 1, '9Z9': 1, 'LPE': 13, 'NAG': 2, 'PCW': 5, 'Y01': 5} Classifications: {'peptide': 2, 'undetermined': 27} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'P5S:plan-2': 1, 'P5S:plan-1': 1, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {'LPE': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.07, per 1000 atoms: 0.21 Number of scatterers: 14841 At special positions: 0 Unit cell: (136.375, 139.648, 137.466, 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 105 16.00 P 21 15.00 O 2677 8.00 N 2241 7.00 C 9797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.02 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.21 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.05 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.02 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.05 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.07 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 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=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2002 " - " ASN A 283 " " NAG A2008 " - " ASN A1375 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " " NAG F 1 " - " ASN B 135 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 559.2 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3254 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 11 sheets defined 67.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 16 through 32 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.865A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 126 through 144 removed outlier: 3.790A pdb=" N MET A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 172 removed outlier: 4.137A pdb=" N ASN A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 186 through 206 Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.655A pdb=" N LEU A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.922A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 223' Processing helix chain 'A' and resid 224 through 227 Processing helix chain 'A' and resid 228 through 229 No H-bonds generated for 'chain 'A' and resid 228 through 229' Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.866A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.750A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 374 removed outlier: 4.072A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.819A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 432 Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 742 through 762 removed outlier: 3.563A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 806 removed outlier: 3.770A pdb=" N VAL A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 825 removed outlier: 3.853A pdb=" N LEU A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 829 No H-bonds generated for 'chain 'A' and resid 827 through 829' Processing helix chain 'A' and resid 830 through 840 removed outlier: 3.872A pdb=" N LEU A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 848 removed outlier: 3.930A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 865 Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.245A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 928 through 940 Processing helix chain 'A' and resid 940 through 971 removed outlier: 3.683A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 977 removed outlier: 3.728A pdb=" N THR A 977 " --> pdb=" O ASP A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 Processing helix chain 'A' and resid 1176 through 1190 removed outlier: 3.613A pdb=" N ASN A1180 " --> pdb=" O LYS A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1209 through 1212 removed outlier: 3.941A pdb=" N GLU A1212 " --> pdb=" O LEU A1209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1209 through 1212' Processing helix chain 'A' and resid 1219 through 1249 Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1257 through 1279 removed outlier: 3.555A pdb=" N LEU A1261 " --> pdb=" O ALA A1257 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A1279 " --> pdb=" O ALA A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1290 removed outlier: 4.146A pdb=" N SER A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 3.872A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix Processing helix chain 'A' and resid 1366 through 1377 removed outlier: 3.742A pdb=" N VAL A1376 " --> pdb=" O ALA A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1417 removed outlier: 3.727A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1444 removed outlier: 3.631A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1467 removed outlier: 3.619A pdb=" N LEU A1449 " --> pdb=" O SER A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 removed outlier: 3.557A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1514 through 1534 removed outlier: 3.696A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A1534 " --> pdb=" O VAL A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1571 through 1575 removed outlier: 4.032A pdb=" N PHE A1574 " --> pdb=" O HIS A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1602 removed outlier: 3.871A pdb=" N THR A1601 " --> pdb=" O ASP A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 4.229A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A1621 " --> pdb=" O ILE A1617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1616 through 1621' Processing helix chain 'A' and resid 1622 through 1626 Processing helix chain 'A' and resid 1627 through 1640 removed outlier: 3.868A pdb=" N THR A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1667 removed outlier: 3.733A pdb=" N LEU A1644 " --> pdb=" O SER A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.112A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1708 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1732 through 1768 Processing helix chain 'A' and resid 1775 through 1790 removed outlier: 3.518A pdb=" N PHE A1779 " --> pdb=" O SER A1775 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A1788 " --> pdb=" O GLU A1784 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A1789 " --> pdb=" O VAL A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1806 removed outlier: 3.897A pdb=" N SER A1803 " --> pdb=" O PHE A1799 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1826 removed outlier: 3.849A pdb=" N ALA A1825 " --> pdb=" O VAL A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1838 through 1851 Processing helix chain 'A' and resid 1853 through 1869 removed outlier: 4.086A pdb=" N ASP A1857 " --> pdb=" O SER A1853 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A1858 " --> pdb=" O GLY A1854 " (cutoff:3.500A) Processing helix chain 'A' and resid 1873 through 1877 removed outlier: 3.894A pdb=" N SER A1876 " --> pdb=" O SER A1873 " (cutoff:3.500A) Processing helix chain 'A' and resid 1883 through 1891 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.779A pdb=" N HIS B 115 " --> pdb=" O THR B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 153 through 192 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.783A pdb=" N PHE A 88 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id=AA4, first strand: chain 'A' and resid 1796 through 1798 Processing sheet with id=AA5, first strand: chain 'A' and resid 1829 through 1831 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.638A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 68 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 51 removed outlier: 4.807A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.642A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.303A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 65 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 48 861 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2240 1.30 - 1.44: 4045 1.44 - 1.58: 8661 1.58 - 1.71: 49 1.71 - 1.85: 172 Bond restraints: 15167 Sorted by residual: bond pdb=" C12 9SL A2001 " pdb=" N11 9SL A2001 " ideal model delta sigma weight residual 1.284 1.503 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C27 P5S A2017 " pdb=" C28 P5S A2017 " ideal model delta sigma weight residual 1.523 1.323 0.200 2.00e-02 2.50e+03 9.99e+01 bond pdb=" C38 P5S A2017 " pdb=" O37 P5S A2017 " ideal model delta sigma weight residual 1.331 1.463 -0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C11 PCW A2027 " pdb=" O3 PCW A2027 " ideal model delta sigma weight residual 1.326 1.458 -0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" C11 PCW A2028 " pdb=" O3 PCW A2028 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.11e+01 ... (remaining 15162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.73: 20361 6.73 - 13.47: 128 13.47 - 20.20: 2 20.20 - 26.93: 0 26.93 - 33.66: 3 Bond angle restraints: 20494 Sorted by residual: angle pdb=" C5 PCW A2028 " pdb=" N PCW A2028 " pdb=" C8 PCW A2028 " ideal model delta sigma weight residual 111.64 77.98 33.66 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C6 PCW A2028 " pdb=" N PCW A2028 " pdb=" C8 PCW A2028 " ideal model delta sigma weight residual 109.11 77.85 31.26 3.00e+00 1.11e-01 1.09e+02 angle pdb=" C7 PCW A2028 " pdb=" N PCW A2028 " pdb=" C8 PCW A2028 " ideal model delta sigma weight residual 108.24 78.03 30.21 3.00e+00 1.11e-01 1.01e+02 angle pdb=" N SER A1418 " pdb=" CA SER A1418 " pdb=" C SER A1418 " ideal model delta sigma weight residual 108.67 122.34 -13.67 1.55e+00 4.16e-01 7.78e+01 angle pdb=" N VAL A1419 " pdb=" CA VAL A1419 " pdb=" C VAL A1419 " ideal model delta sigma weight residual 110.53 118.60 -8.07 9.40e-01 1.13e+00 7.36e+01 ... (remaining 20489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.08: 8626 32.08 - 64.17: 368 64.17 - 96.25: 29 96.25 - 128.33: 5 128.33 - 160.42: 2 Dihedral angle restraints: 9030 sinusoidal: 3999 harmonic: 5031 Sorted by residual: dihedral pdb=" CB CYS A1715 " pdb=" SG CYS A1715 " pdb=" SG CYS A1730 " pdb=" CB CYS A1730 " ideal model delta sinusoidal sigma weight residual 93.00 34.58 58.42 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual 93.00 148.71 -55.71 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CA SER A1362 " pdb=" C SER A1362 " pdb=" N GLN A1363 " pdb=" CA GLN A1363 " ideal model delta harmonic sigma weight residual 180.00 155.78 24.22 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 9027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2197 0.146 - 0.293: 86 0.293 - 0.439: 22 0.439 - 0.586: 6 0.586 - 0.732: 2 Chirality restraints: 2313 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.78e+02 chirality pdb=" C1 NAG A2008 " pdb=" ND2 ASN A1375 " pdb=" C2 NAG A2008 " pdb=" O5 NAG A2008 " both_signs ideal model delta sigma weight residual False -2.40 -3.13 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 135 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.76e+00 ... (remaining 2310 not shown) Planarity restraints: 2429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2008 " 0.202 2.00e-02 2.50e+03 1.68e-01 3.52e+02 pdb=" C7 NAG A2008 " -0.054 2.00e-02 2.50e+03 pdb=" C8 NAG A2008 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG A2008 " -0.275 2.00e-02 2.50e+03 pdb=" O7 NAG A2008 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1375 " 0.114 2.00e-02 2.50e+03 1.08e-01 1.46e+02 pdb=" CG ASN A1375 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A1375 " -0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN A1375 " -0.149 2.00e-02 2.50e+03 pdb=" C1 NAG A2008 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 93 " -0.059 2.00e-02 2.50e+03 6.75e-02 5.69e+01 pdb=" CG ASN B 93 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 93 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 93 " 0.111 2.00e-02 2.50e+03 pdb=" C1 NAG B 301 " -0.079 2.00e-02 2.50e+03 ... (remaining 2426 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 29 2.39 - 3.02: 9270 3.02 - 3.64: 21319 3.64 - 4.27: 33128 4.27 - 4.90: 54400 Nonbonded interactions: 118146 Sorted by model distance: nonbonded pdb=" CE2 TYR A1602 " pdb=" CE1 PHE A1603 " model vdw 1.761 3.640 nonbonded pdb=" CD2 TYR A1602 " pdb=" CE1 PHE A1603 " model vdw 1.922 3.640 nonbonded pdb=" OD1 ASN A1366 " pdb=" OG SER A1368 " model vdw 2.110 3.040 nonbonded pdb=" CD2 TYR A1602 " pdb=" CD1 PHE A1603 " model vdw 2.182 3.640 nonbonded pdb=" O ASP A1673 " pdb=" OD1 ASP A1673 " model vdw 2.207 3.040 ... (remaining 118141 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.14 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.450 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 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 : 0.013 0.774 15191 Z= 0.872 Angle : 1.512 64.948 20549 Z= 0.726 Chirality : 0.077 0.732 2313 Planarity : 0.007 0.168 2421 Dihedral : 16.693 160.415 5743 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 1.63 % Allowed : 12.56 % Favored : 85.82 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 7.41 % 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: -1.26 (0.20), residues: 1700 helix: -0.05 (0.16), residues: 1003 sheet: -2.01 (0.39), residues: 146 loop : -1.78 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 117 TYR 0.032 0.002 TYR A1413 PHE 0.030 0.002 PHE A1661 TRP 0.050 0.002 TRP A 933 HIS 0.006 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.01059 / 0.57 (15167) covalent geometry : angle 1.35083 / 0.68 (20494) SS BOND : bond 0.05638 / 2.91 ( 11) SS BOND : angle 11.06625 / 3.16 ( 22) hydrogen bonds : bond 0.15523 / 10.03 ( 861) hydrogen bonds : angle 6.23261 / 4.42 ( 2448) Misc. bond : bond 0.55310 / 34.49 ( 2) link_BETA1-4 : bond 0.05823 / 3.23 ( 3) link_BETA1-4 : angle 22.54152 / 16.34 ( 9) link_NAG-ASN : bond 0.12925 / 8.99 ( 8) link_NAG-ASN : angle 9.86795 / 7.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 280 time to evaluate : 0.636 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 53 LEU cc_start: 0.8225 (mt) cc_final: 0.7928 (mt) REVERT: A 70 MET cc_start: 0.4931 (mmt) cc_final: 0.4270 (tpp) REVERT: A 86 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8067 (mmmm) REVERT: A 91 LEU cc_start: 0.8499 (mt) cc_final: 0.8260 (mt) REVERT: A 147 ASN cc_start: 0.8463 (t0) cc_final: 0.7960 (p0) REVERT: A 184 LEU cc_start: 0.9018 (mm) cc_final: 0.8472 (tm) REVERT: A 190 TRP cc_start: 0.7775 (m100) cc_final: 0.7547 (m100) REVERT: A 214 ARG cc_start: 0.8669 (mtp180) cc_final: 0.8244 (mtp85) REVERT: A 217 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7508 (mtm180) REVERT: A 241 SER cc_start: 0.8220 (m) cc_final: 0.7926 (t) REVERT: A 268 MET cc_start: 0.8039 (ttp) cc_final: 0.7779 (ttp) REVERT: A 380 ILE cc_start: 0.8605 (pt) cc_final: 0.8279 (mp) REVERT: A 742 MET cc_start: 0.4845 (mtt) cc_final: 0.4080 (tpp) REVERT: A 761 MET cc_start: 0.8146 (mtm) cc_final: 0.7875 (mtp) REVERT: A 763 MET cc_start: 0.8393 (mtt) cc_final: 0.8108 (mmm) REVERT: A 841 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.8066 (mtt90) REVERT: A 932 MET cc_start: 0.8301 (ttp) cc_final: 0.8051 (ttm) REVERT: A 950 MET cc_start: 0.8556 (mtm) cc_final: 0.8097 (mtp) REVERT: A 1195 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7272 (mp0) REVERT: A 1201 MET cc_start: 0.8610 (mmp) cc_final: 0.8369 (mmp) REVERT: A 1273 LEU cc_start: 0.8681 (tp) cc_final: 0.8006 (tp) REVERT: A 1474 MET cc_start: 0.8549 (mtt) cc_final: 0.8250 (mtp) REVERT: A 1543 MET cc_start: 0.7496 (tpp) cc_final: 0.7279 (tpp) REVERT: A 1548 TYR cc_start: 0.8389 (t80) cc_final: 0.8120 (t80) REVERT: A 1732 ASN cc_start: 0.8049 (t0) cc_final: 0.7758 (t0) REVERT: B 72 ARG cc_start: 0.8481 (ttt90) cc_final: 0.8240 (ttt180) REVERT: B 152 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7616 (ttp80) outliers start: 25 outliers final: 10 residues processed: 301 average time/residue: 0.5042 time to fit residues: 169.3950 Evaluate side-chains 197 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1450 ASN Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 139 ASN A 278 ASN A 323 GLN A 365 ASN A 408 GLN A 412 ASN A 425 GLN A 757 ASN A 809 ASN A 853 ASN A 861 ASN A 909 HIS A 941 GLN A 961 ASN A 975 ASN A1378 GLN A1478 GLN A1494 GLN A1502 ASN A1528 ASN A1539 GLN A1551 ASN A1871 ASN B 102 GLN B 115 HIS C 53 ASN C 70 GLN C 82 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.160769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108411 restraints weight = 43871.534| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.98 r_work: 0.3199 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15191 Z= 0.155 Angle : 0.733 20.418 20549 Z= 0.349 Chirality : 0.045 0.400 2313 Planarity : 0.004 0.056 2421 Dihedral : 14.922 169.061 2457 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 3.71 % Allowed : 18.48 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.18 (0.20), residues: 1700 helix: 1.11 (0.16), residues: 1006 sheet: -1.49 (0.40), residues: 142 loop : -1.22 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1613 TYR 0.020 0.002 TYR A1572 PHE 0.030 0.002 PHE C 63 TRP 0.033 0.001 TRP A 933 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (15167) covalent geometry : angle 0.69939 / 0.34 (20494) SS BOND : bond 0.00610 / 0.35 ( 11) SS BOND : angle 1.76313 / 0.82 ( 22) hydrogen bonds : bond 0.05154 / 3.37 ( 861) hydrogen bonds : angle 4.65691 / 3.31 ( 2448) Misc. bond : bond 0.00428 / 0.27 ( 2) link_BETA1-4 : bond 0.00300 / 0.17 ( 3) link_BETA1-4 : angle 9.45248 / 6.86 ( 9) link_NAG-ASN : bond 0.00808 / 0.51 ( 8) link_NAG-ASN : angle 2.45621 / 1.67 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5171 (mmt) cc_final: 0.4607 (tpp) REVERT: A 147 ASN cc_start: 0.8386 (t0) cc_final: 0.8023 (p0) REVERT: A 184 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8680 (tm) REVERT: A 190 TRP cc_start: 0.7836 (m100) cc_final: 0.7634 (m100) REVERT: A 214 ARG cc_start: 0.8473 (mtp180) cc_final: 0.8241 (mtm180) REVERT: A 217 ARG cc_start: 0.8363 (mtp180) cc_final: 0.7931 (mtm110) REVERT: A 742 MET cc_start: 0.4657 (mtt) cc_final: 0.4127 (ttt) REVERT: A 763 MET cc_start: 0.8743 (mtt) cc_final: 0.8505 (mmm) REVERT: A 841 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8379 (mtt90) REVERT: A 950 MET cc_start: 0.9193 (mtm) cc_final: 0.8865 (mtp) REVERT: A 1227 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: A 1267 ASP cc_start: 0.8158 (t70) cc_final: 0.7846 (t0) REVERT: A 1474 MET cc_start: 0.8858 (mtt) cc_final: 0.8595 (mtm) REVERT: A 1732 ASN cc_start: 0.8447 (t0) cc_final: 0.8078 (t0) REVERT: A 1863 MET cc_start: -0.3322 (mpp) cc_final: -0.3609 (mmt) REVERT: C 63 PHE cc_start: 0.8633 (t80) cc_final: 0.8375 (t80) REVERT: C 69 TYR cc_start: 0.4419 (t80) cc_final: 0.3447 (t80) REVERT: C 80 PHE cc_start: 0.5786 (p90) cc_final: 0.5550 (p90) REVERT: C 84 ARG cc_start: 0.8323 (ttt180) cc_final: 0.8115 (ttm170) outliers start: 57 outliers final: 16 residues processed: 247 average time/residue: 0.4346 time to fit residues: 121.2514 Evaluate side-chains 196 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.160708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108348 restraints weight = 35883.392| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.22 r_work: 0.3223 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15191 Z= 0.138 Angle : 0.635 12.154 20549 Z= 0.310 Chirality : 0.041 0.325 2313 Planarity : 0.004 0.049 2421 Dihedral : 13.883 167.417 2439 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 3.84 % Allowed : 20.04 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.68 (0.21), residues: 1700 helix: 1.54 (0.16), residues: 1001 sheet: -1.48 (0.39), residues: 148 loop : -0.97 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 26 TYR 0.015 0.001 TYR A1573 PHE 0.023 0.001 PHE A 733 TRP 0.018 0.001 TRP A 933 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (15167) covalent geometry : angle 0.62318 / 0.31 (20494) SS BOND : bond 0.00286 / 0.20 ( 11) SS BOND : angle 1.17330 / 0.59 ( 22) hydrogen bonds : bond 0.04650 / 3.03 ( 861) hydrogen bonds : angle 4.39833 / 3.11 ( 2448) Misc. bond : bond 0.00061 / 0.04 ( 2) link_BETA1-4 : bond 0.00618 / 0.35 ( 3) link_BETA1-4 : angle 4.12218 / 2.89 ( 9) link_NAG-ASN : bond 0.00637 / 0.39 ( 8) link_NAG-ASN : angle 2.55361 / 1.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7272 (pt) REVERT: A 147 ASN cc_start: 0.8324 (t0) cc_final: 0.8010 (p0) REVERT: A 184 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8666 (tm) REVERT: A 192 ASP cc_start: 0.8217 (t70) cc_final: 0.7964 (t0) REVERT: A 214 ARG cc_start: 0.8338 (mtp180) cc_final: 0.7974 (mtp180) REVERT: A 217 ARG cc_start: 0.8313 (mtp180) cc_final: 0.7940 (mtm180) REVERT: A 379 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8431 (tmm) REVERT: A 742 MET cc_start: 0.4839 (mtt) cc_final: 0.4281 (ttt) REVERT: A 841 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8365 (mtt90) REVERT: A 950 MET cc_start: 0.9117 (mtm) cc_final: 0.8851 (mtp) REVERT: A 1227 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: A 1230 ASP cc_start: 0.7905 (m-30) cc_final: 0.7554 (t0) REVERT: A 1267 ASP cc_start: 0.8208 (t70) cc_final: 0.7912 (t0) REVERT: A 1474 MET cc_start: 0.8814 (mtt) cc_final: 0.8566 (mtm) REVERT: A 1732 ASN cc_start: 0.8423 (t0) cc_final: 0.8123 (t0) REVERT: A 1830 MET cc_start: -0.1152 (tmm) cc_final: -0.1364 (ptt) REVERT: A 1856 MET cc_start: 0.0401 (mpm) cc_final: -0.0667 (mtt) REVERT: A 1863 MET cc_start: -0.3526 (mpp) cc_final: -0.3788 (mmt) REVERT: C 31 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7960 (tm-30) REVERT: C 67 TRP cc_start: 0.5513 (m100) cc_final: 0.5190 (m100) REVERT: C 69 TYR cc_start: 0.4347 (t80) cc_final: 0.3424 (t80) REVERT: C 80 PHE cc_start: 0.5764 (p90) cc_final: 0.5047 (p90) REVERT: C 136 HIS cc_start: 0.8658 (m-70) cc_final: 0.8369 (t-90) outliers start: 59 outliers final: 22 residues processed: 235 average time/residue: 0.4597 time to fit residues: 122.3929 Evaluate side-chains 205 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 138 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 131 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 861 ASN ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.159946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.108309 restraints weight = 49576.589| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.85 r_work: 0.3189 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15191 Z= 0.144 Angle : 0.627 12.049 20549 Z= 0.307 Chirality : 0.042 0.346 2313 Planarity : 0.004 0.049 2421 Dihedral : 13.333 167.847 2439 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 4.62 % Allowed : 20.43 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.93 (0.21), residues: 1700 helix: 1.74 (0.16), residues: 995 sheet: -1.34 (0.42), residues: 145 loop : -0.85 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 135 TYR 0.018 0.001 TYR A1573 PHE 0.025 0.001 PHE A1452 TRP 0.012 0.001 TRP A 933 HIS 0.004 0.001 HIS A1571 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (15167) covalent geometry : angle 0.61891 / 0.30 (20494) SS BOND : bond 0.00273 / 0.18 ( 11) SS BOND : angle 1.10973 / 0.56 ( 22) hydrogen bonds : bond 0.04478 / 2.93 ( 861) hydrogen bonds : angle 4.25442 / 3.00 ( 2448) Misc. bond : bond 0.00435 / 0.27 ( 2) link_BETA1-4 : bond 0.00711 / 0.40 ( 3) link_BETA1-4 : angle 2.90693 / 1.97 ( 9) link_NAG-ASN : bond 0.00582 / 0.36 ( 8) link_NAG-ASN : angle 2.34867 / 1.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 199 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5100 (mmt) cc_final: 0.4682 (mmt) REVERT: A 147 ASN cc_start: 0.8304 (t0) cc_final: 0.7984 (p0) REVERT: A 152 THR cc_start: 0.8450 (m) cc_final: 0.8099 (p) REVERT: A 184 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8648 (tm) REVERT: A 214 ARG cc_start: 0.8393 (mtp180) cc_final: 0.8060 (mtp85) REVERT: A 217 ARG cc_start: 0.8329 (mtp180) cc_final: 0.7930 (mtm110) REVERT: A 379 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8395 (tmm) REVERT: A 742 MET cc_start: 0.4760 (mtt) cc_final: 0.4554 (ttm) REVERT: A 809 ASN cc_start: 0.8710 (m110) cc_final: 0.8314 (m110) REVERT: A 841 ARG cc_start: 0.8686 (ttm-80) cc_final: 0.8423 (mtt90) REVERT: A 950 MET cc_start: 0.9137 (mtm) cc_final: 0.8725 (mtp) REVERT: A 952 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8339 (tmm) REVERT: A 1227 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: A 1267 ASP cc_start: 0.8220 (t70) cc_final: 0.7929 (t0) REVERT: A 1474 MET cc_start: 0.8840 (mtt) cc_final: 0.8569 (mtm) REVERT: A 1655 MET cc_start: 0.9046 (mtp) cc_final: 0.8822 (mtm) REVERT: A 1732 ASN cc_start: 0.8444 (t0) cc_final: 0.8150 (t0) REVERT: A 1856 MET cc_start: 0.0278 (mpm) cc_final: -0.0755 (mtt) REVERT: A 1863 MET cc_start: -0.3633 (OUTLIER) cc_final: -0.3883 (mmt) REVERT: C 47 ARG cc_start: 0.5706 (OUTLIER) cc_final: 0.5298 (tpt-90) REVERT: C 67 TRP cc_start: 0.5758 (m100) cc_final: 0.5537 (m100) REVERT: C 80 PHE cc_start: 0.5427 (p90) cc_final: 0.4998 (p90) REVERT: C 136 HIS cc_start: 0.8517 (m-70) cc_final: 0.8227 (t-90) outliers start: 71 outliers final: 27 residues processed: 246 average time/residue: 0.4581 time to fit residues: 126.9874 Evaluate side-chains 215 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 106 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 59 optimal weight: 0.0050 chunk 141 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.159821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104654 restraints weight = 39340.623| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.50 r_work: 0.3216 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15191 Z= 0.151 Angle : 0.616 10.091 20549 Z= 0.303 Chirality : 0.041 0.358 2313 Planarity : 0.004 0.048 2421 Dihedral : 13.219 169.730 2439 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 4.55 % Allowed : 21.08 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.96 (0.21), residues: 1700 helix: 1.76 (0.16), residues: 993 sheet: -1.16 (0.42), residues: 145 loop : -0.87 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1613 TYR 0.019 0.001 TYR A1573 PHE 0.023 0.001 PHE A 733 TRP 0.009 0.001 TRP A 190 HIS 0.004 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15167) covalent geometry : angle 0.60906 / 0.30 (20494) SS BOND : bond 0.00358 / 0.23 ( 11) SS BOND : angle 1.04913 / 0.54 ( 22) hydrogen bonds : bond 0.04432 / 2.90 ( 861) hydrogen bonds : angle 4.24899 / 3.00 ( 2448) Misc. bond : bond 0.00394 / 0.25 ( 2) link_BETA1-4 : bond 0.00978 / 0.55 ( 3) link_BETA1-4 : angle 2.11832 / 1.39 ( 9) link_NAG-ASN : bond 0.00601 / 0.37 ( 8) link_NAG-ASN : angle 2.33799 / 1.60 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 195 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5035 (mmt) cc_final: 0.4253 (tpt) REVERT: A 141 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8681 (mm) REVERT: A 147 ASN cc_start: 0.8248 (t0) cc_final: 0.7992 (p0) REVERT: A 184 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8609 (tm) REVERT: A 214 ARG cc_start: 0.8328 (mtp180) cc_final: 0.7990 (mtp85) REVERT: A 217 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7849 (mtm110) REVERT: A 379 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8314 (tmm) REVERT: A 809 ASN cc_start: 0.8762 (m110) cc_final: 0.8376 (m110) REVERT: A 841 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8437 (mtt90) REVERT: A 950 MET cc_start: 0.9062 (mtm) cc_final: 0.8714 (mtp) REVERT: A 1227 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: A 1230 ASP cc_start: 0.7957 (t0) cc_final: 0.7665 (t0) REVERT: A 1267 ASP cc_start: 0.8156 (t70) cc_final: 0.7883 (t0) REVERT: A 1474 MET cc_start: 0.8817 (mtt) cc_final: 0.8536 (mtm) REVERT: A 1732 ASN cc_start: 0.8447 (t0) cc_final: 0.8146 (t0) REVERT: A 1856 MET cc_start: -0.0096 (mpm) cc_final: -0.1060 (mtt) REVERT: A 1863 MET cc_start: -0.3832 (OUTLIER) cc_final: -0.4058 (mmt) REVERT: C 47 ARG cc_start: 0.5753 (OUTLIER) cc_final: 0.5501 (tpt-90) REVERT: C 67 TRP cc_start: 0.5487 (m100) cc_final: 0.5266 (m100) REVERT: C 80 PHE cc_start: 0.5519 (p90) cc_final: 0.5015 (p90) REVERT: C 113 MET cc_start: 0.5205 (tmm) cc_final: 0.4808 (tmt) REVERT: C 115 ARG cc_start: 0.6666 (ptp-110) cc_final: 0.6365 (mtm-85) REVERT: C 128 TYR cc_start: 0.7740 (m-10) cc_final: 0.6949 (m-10) outliers start: 70 outliers final: 36 residues processed: 244 average time/residue: 0.4560 time to fit residues: 124.8623 Evaluate side-chains 220 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 48 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN ** A1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.156541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103473 restraints weight = 40505.526| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.46 r_work: 0.3129 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 15191 Z= 0.277 Angle : 0.721 11.203 20549 Z= 0.357 Chirality : 0.045 0.336 2313 Planarity : 0.004 0.046 2421 Dihedral : 14.015 172.890 2439 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 4.81 % Allowed : 21.99 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.62 (0.21), residues: 1700 helix: 1.47 (0.16), residues: 991 sheet: -1.26 (0.42), residues: 145 loop : -0.99 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 135 TYR 0.023 0.002 TYR A1573 PHE 0.028 0.002 PHE C 63 TRP 0.009 0.002 TRP A1700 HIS 0.007 0.002 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.28 (15167) covalent geometry : angle 0.71136 / 0.35 (20494) SS BOND : bond 0.00369 / 0.26 ( 11) SS BOND : angle 2.05189 / 0.97 ( 22) hydrogen bonds : bond 0.05249 / 3.45 ( 861) hydrogen bonds : angle 4.44256 / 3.13 ( 2448) Misc. bond : bond 0.01000 / 0.58 ( 2) link_BETA1-4 : bond 0.00690 / 0.38 ( 3) link_BETA1-4 : angle 2.82484 / 1.76 ( 9) link_NAG-ASN : bond 0.00722 / 0.44 ( 8) link_NAG-ASN : angle 2.55188 / 1.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 177 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.4849 (mmt) cc_final: 0.4262 (mmt) REVERT: A 184 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8658 (tm) REVERT: A 214 ARG cc_start: 0.8398 (mtp180) cc_final: 0.8103 (mtp85) REVERT: A 217 ARG cc_start: 0.8363 (mtp180) cc_final: 0.7936 (mtm110) REVERT: A 379 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8321 (tmm) REVERT: A 809 ASN cc_start: 0.8814 (m110) cc_final: 0.8429 (m110) REVERT: A 841 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8496 (mtt90) REVERT: A 950 MET cc_start: 0.9144 (mtm) cc_final: 0.8797 (mtp) REVERT: A 1227 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: A 1230 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7759 (t0) REVERT: A 1305 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6198 (mp0) REVERT: A 1474 MET cc_start: 0.8800 (mtt) cc_final: 0.8516 (mtm) REVERT: A 1732 ASN cc_start: 0.8573 (t0) cc_final: 0.8351 (t0) REVERT: C 80 PHE cc_start: 0.5397 (p90) cc_final: 0.4805 (p90) REVERT: C 84 ARG cc_start: 0.6535 (ttm170) cc_final: 0.5965 (pmt-80) REVERT: C 128 TYR cc_start: 0.8124 (m-10) cc_final: 0.7750 (m-10) outliers start: 74 outliers final: 43 residues processed: 231 average time/residue: 0.4408 time to fit residues: 114.9553 Evaluate side-chains 215 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 129 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 37 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 774 ASN A1502 ASN ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.159389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.105590 restraints weight = 48507.229| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.63 r_work: 0.3174 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15191 Z= 0.141 Angle : 0.632 10.598 20549 Z= 0.313 Chirality : 0.041 0.333 2313 Planarity : 0.004 0.048 2421 Dihedral : 13.476 163.740 2439 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 3.97 % Allowed : 23.10 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.98 (0.21), residues: 1700 helix: 1.77 (0.16), residues: 987 sheet: -1.13 (0.43), residues: 145 loop : -0.82 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 135 TYR 0.023 0.001 TYR A1573 PHE 0.024 0.001 PHE A 733 TRP 0.024 0.001 TRP C 67 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (15167) covalent geometry : angle 0.62447 / 0.31 (20494) SS BOND : bond 0.00274 / 0.19 ( 11) SS BOND : angle 1.34491 / 0.65 ( 22) hydrogen bonds : bond 0.04452 / 2.91 ( 861) hydrogen bonds : angle 4.25498 / 3.00 ( 2448) Misc. bond : bond 0.00366 / 0.23 ( 2) link_BETA1-4 : bond 0.00684 / 0.38 ( 3) link_BETA1-4 : angle 2.45205 / 1.65 ( 9) link_NAG-ASN : bond 0.00610 / 0.38 ( 8) link_NAG-ASN : angle 2.36466 / 1.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5010 (mmt) cc_final: 0.4509 (mmt) REVERT: A 184 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8637 (tm) REVERT: A 214 ARG cc_start: 0.8389 (mtp180) cc_final: 0.8078 (mtp85) REVERT: A 217 ARG cc_start: 0.8332 (mtp180) cc_final: 0.7904 (mtm110) REVERT: A 244 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7987 (ttpp) REVERT: A 379 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8317 (tmm) REVERT: A 768 MET cc_start: 0.7045 (mtm) cc_final: 0.6833 (mtt) REVERT: A 809 ASN cc_start: 0.8811 (m110) cc_final: 0.8162 (m110) REVERT: A 841 ARG cc_start: 0.8752 (ttm-80) cc_final: 0.8486 (mtt90) REVERT: A 1227 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: A 1230 ASP cc_start: 0.8020 (t0) cc_final: 0.7752 (t0) REVERT: A 1474 MET cc_start: 0.8822 (mtt) cc_final: 0.8526 (mtm) REVERT: A 1732 ASN cc_start: 0.8531 (t0) cc_final: 0.8199 (t0) REVERT: A 1760 LEU cc_start: 0.8307 (tp) cc_final: 0.8089 (tt) REVERT: A 1856 MET cc_start: 0.2205 (mmm) cc_final: 0.0345 (mtp) REVERT: B 34 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7979 (mtm) REVERT: C 67 TRP cc_start: 0.5633 (m100) cc_final: 0.5230 (m100) REVERT: C 80 PHE cc_start: 0.5361 (p90) cc_final: 0.4056 (p90) REVERT: C 84 ARG cc_start: 0.6461 (ttm170) cc_final: 0.6038 (pmt-80) REVERT: C 113 MET cc_start: 0.5491 (tmt) cc_final: 0.5237 (tmt) REVERT: C 137 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6604 (tpt90) outliers start: 61 outliers final: 28 residues processed: 232 average time/residue: 0.4646 time to fit residues: 121.0901 Evaluate side-chains 214 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 137 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 139 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.157778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.104594 restraints weight = 53923.747| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.78 r_work: 0.3146 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15191 Z= 0.203 Angle : 0.683 10.595 20549 Z= 0.333 Chirality : 0.043 0.333 2313 Planarity : 0.004 0.050 2421 Dihedral : 13.523 150.348 2439 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 3.90 % Allowed : 23.03 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.85 (0.21), residues: 1700 helix: 1.64 (0.16), residues: 993 sheet: -1.27 (0.42), residues: 145 loop : -0.84 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 135 TYR 0.027 0.002 TYR A1573 PHE 0.027 0.002 PHE A1452 TRP 0.019 0.001 TRP A1408 HIS 0.005 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (15167) covalent geometry : angle 0.67390 / 0.33 (20494) SS BOND : bond 0.00280 / 0.20 ( 11) SS BOND : angle 1.65206 / 0.78 ( 22) hydrogen bonds : bond 0.04800 / 3.14 ( 861) hydrogen bonds : angle 4.32186 / 3.05 ( 2448) Misc. bond : bond 0.00467 / 0.29 ( 2) link_BETA1-4 : bond 0.00736 / 0.41 ( 3) link_BETA1-4 : angle 2.70905 / 1.75 ( 9) link_NAG-ASN : bond 0.00665 / 0.41 ( 8) link_NAG-ASN : angle 2.47929 / 1.69 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5005 (mmt) cc_final: 0.4426 (mmt) REVERT: A 184 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8598 (tm) REVERT: A 214 ARG cc_start: 0.8435 (mtp180) cc_final: 0.8139 (mtp85) REVERT: A 217 ARG cc_start: 0.8309 (mtp180) cc_final: 0.7861 (mtm110) REVERT: A 244 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8105 (ttpp) REVERT: A 379 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8411 (tmm) REVERT: A 768 MET cc_start: 0.7127 (mtm) cc_final: 0.6825 (mtt) REVERT: A 809 ASN cc_start: 0.8794 (m110) cc_final: 0.8429 (m110) REVERT: A 841 ARG cc_start: 0.8836 (ttm-80) cc_final: 0.8488 (mtt90) REVERT: A 950 MET cc_start: 0.9090 (mtm) cc_final: 0.8704 (mtp) REVERT: A 1227 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: A 1230 ASP cc_start: 0.8055 (t0) cc_final: 0.7758 (t0) REVERT: A 1474 MET cc_start: 0.8806 (mtt) cc_final: 0.8493 (mtm) REVERT: A 1617 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8468 (mt) REVERT: A 1732 ASN cc_start: 0.8541 (t0) cc_final: 0.8281 (t0) REVERT: A 1856 MET cc_start: 0.2222 (mmm) cc_final: 0.0301 (mtp) REVERT: B 34 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8068 (mtm) REVERT: C 67 TRP cc_start: 0.5605 (m100) cc_final: 0.5261 (m100) REVERT: C 80 PHE cc_start: 0.5364 (p90) cc_final: 0.4521 (p90) REVERT: C 113 MET cc_start: 0.5539 (tmt) cc_final: 0.5248 (tmt) outliers start: 60 outliers final: 38 residues processed: 226 average time/residue: 0.4535 time to fit residues: 114.9110 Evaluate side-chains 224 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 7 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 0.0070 chunk 134 optimal weight: 0.0870 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN A1539 GLN B 50 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.161551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108633 restraints weight = 54183.529| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 4.13 r_work: 0.3190 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15191 Z= 0.115 Angle : 0.625 12.599 20549 Z= 0.304 Chirality : 0.040 0.326 2313 Planarity : 0.004 0.053 2421 Dihedral : 12.740 162.564 2439 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 2.08 % Allowed : 25.50 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.20 (0.21), residues: 1700 helix: 1.94 (0.16), residues: 986 sheet: -1.06 (0.43), residues: 145 loop : -0.70 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 135 TYR 0.017 0.001 TYR A1573 PHE 0.024 0.001 PHE A 733 TRP 0.036 0.001 TRP A1408 HIS 0.003 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (15167) covalent geometry : angle 0.61866 / 0.30 (20494) SS BOND : bond 0.00233 / 0.16 ( 11) SS BOND : angle 0.95675 / 0.50 ( 22) hydrogen bonds : bond 0.04000 / 2.60 ( 861) hydrogen bonds : angle 4.17112 / 2.95 ( 2448) Misc. bond : bond 0.00284 / 0.18 ( 2) link_BETA1-4 : bond 0.00687 / 0.38 ( 3) link_BETA1-4 : angle 2.18575 / 1.51 ( 9) link_NAG-ASN : bond 0.00585 / 0.37 ( 8) link_NAG-ASN : angle 2.21741 / 1.54 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5209 (mmt) cc_final: 0.4328 (tpt) REVERT: A 184 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8591 (tm) REVERT: A 217 ARG cc_start: 0.8339 (mtp180) cc_final: 0.7864 (mtm110) REVERT: A 379 MET cc_start: 0.8655 (tmm) cc_final: 0.8255 (tmm) REVERT: A 809 ASN cc_start: 0.8722 (m110) cc_final: 0.8276 (m-40) REVERT: A 1227 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: A 1230 ASP cc_start: 0.7939 (t0) cc_final: 0.7654 (t0) REVERT: A 1474 MET cc_start: 0.8824 (mtt) cc_final: 0.8489 (mtm) REVERT: A 1732 ASN cc_start: 0.8404 (t0) cc_final: 0.8104 (t0) REVERT: A 1856 MET cc_start: 0.2270 (mmm) cc_final: 0.0398 (mtp) REVERT: C 67 TRP cc_start: 0.5591 (m100) cc_final: 0.4998 (m100) REVERT: C 80 PHE cc_start: 0.5352 (p90) cc_final: 0.4417 (p90) REVERT: C 84 ARG cc_start: 0.6628 (ttm170) cc_final: 0.6165 (pmt-80) REVERT: C 115 ARG cc_start: 0.6277 (ptp-110) cc_final: 0.6048 (mpp80) outliers start: 32 outliers final: 18 residues processed: 222 average time/residue: 0.5078 time to fit residues: 126.2603 Evaluate side-chains 200 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 139 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.159623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.107355 restraints weight = 51902.198| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 4.09 r_work: 0.3162 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15191 Z= 0.154 Angle : 0.674 11.482 20549 Z= 0.330 Chirality : 0.042 0.361 2313 Planarity : 0.004 0.058 2421 Dihedral : 12.615 156.493 2439 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 1.50 % Allowed : 26.15 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.12 (0.21), residues: 1700 helix: 1.87 (0.16), residues: 985 sheet: -1.05 (0.43), residues: 145 loop : -0.72 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 135 TYR 0.018 0.001 TYR A1573 PHE 0.032 0.001 PHE A 811 TRP 0.025 0.001 TRP A1408 HIS 0.004 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (15167) covalent geometry : angle 0.66722 / 0.33 (20494) SS BOND : bond 0.00278 / 0.19 ( 11) SS BOND : angle 1.30217 / 0.63 ( 22) hydrogen bonds : bond 0.04327 / 2.83 ( 861) hydrogen bonds : angle 4.23380 / 2.99 ( 2448) Misc. bond : bond 0.00389 / 0.24 ( 2) link_BETA1-4 : bond 0.00833 / 0.46 ( 3) link_BETA1-4 : angle 2.24049 / 1.50 ( 9) link_NAG-ASN : bond 0.00591 / 0.37 ( 8) link_NAG-ASN : angle 2.30031 / 1.57 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5101 (mmt) cc_final: 0.4193 (tpt) REVERT: A 184 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8551 (tm) REVERT: A 217 ARG cc_start: 0.8316 (mtp180) cc_final: 0.7818 (mtm110) REVERT: A 379 MET cc_start: 0.8703 (tmm) cc_final: 0.8311 (tmm) REVERT: A 809 ASN cc_start: 0.8738 (m110) cc_final: 0.8289 (m-40) REVERT: A 1227 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: A 1230 ASP cc_start: 0.8110 (t0) cc_final: 0.7801 (t0) REVERT: A 1474 MET cc_start: 0.8806 (mtt) cc_final: 0.8498 (mtm) REVERT: A 1732 ASN cc_start: 0.8473 (t0) cc_final: 0.8175 (t0) REVERT: A 1781 MET cc_start: -0.0642 (pp-130) cc_final: -0.1530 (ttt) REVERT: A 1856 MET cc_start: 0.2291 (mmm) cc_final: 0.0404 (mtp) REVERT: C 67 TRP cc_start: 0.5607 (m100) cc_final: 0.4987 (m100) REVERT: C 80 PHE cc_start: 0.5318 (p90) cc_final: 0.4429 (p90) REVERT: C 84 ARG cc_start: 0.6618 (ttm170) cc_final: 0.6180 (pmt-80) outliers start: 23 outliers final: 19 residues processed: 202 average time/residue: 0.4993 time to fit residues: 112.9407 Evaluate side-chains 195 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1875 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 87 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 83 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 133 optimal weight: 0.0970 chunk 154 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.161559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.109161 restraints weight = 53605.130| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 4.14 r_work: 0.3200 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15191 Z= 0.124 Angle : 0.655 11.797 20549 Z= 0.321 Chirality : 0.041 0.343 2313 Planarity : 0.004 0.059 2421 Dihedral : 12.118 159.492 2439 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 1.69 % Allowed : 26.09 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.28 (0.21), residues: 1700 helix: 1.95 (0.16), residues: 983 sheet: -0.78 (0.45), residues: 139 loop : -0.63 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 135 TYR 0.018 0.001 TYR A1573 PHE 0.025 0.001 PHE A 733 TRP 0.027 0.001 TRP A1408 HIS 0.002 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15167) covalent geometry : angle 0.64918 / 0.32 (20494) SS BOND : bond 0.00219 / 0.16 ( 11) SS BOND : angle 0.96680 / 0.50 ( 22) hydrogen bonds : bond 0.04016 / 2.60 ( 861) hydrogen bonds : angle 4.18251 / 2.95 ( 2448) Misc. bond : bond 0.00315 / 0.20 ( 2) link_BETA1-4 : bond 0.00759 / 0.42 ( 3) link_BETA1-4 : angle 2.04714 / 1.40 ( 9) link_NAG-ASN : bond 0.00571 / 0.36 ( 8) link_NAG-ASN : angle 2.18893 / 1.51 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5858.88 seconds wall clock time: 100 minutes 23.47 seconds (6023.47 seconds total)