Starting phenix.real_space_refine on Wed Sep 17 22:08:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyk_43663/09_2025/8vyk_43663.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyk_43663/09_2025/8vyk_43663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vyk_43663/09_2025/8vyk_43663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyk_43663/09_2025/8vyk_43663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vyk_43663/09_2025/8vyk_43663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyk_43663/09_2025/8vyk_43663.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 2 5.49 5 S 89 5.16 5 C 7751 2.51 5 N 1804 2.21 5 O 2075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11721 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11216 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1395, 11210 Classifications: {'peptide': 1395} Link IDs: {'PTRANS': 49, 'TRANS': 1345} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1395, 11210 Classifications: {'peptide': 1395} Link IDs: {'PTRANS': 49, 'TRANS': 1345} Chain breaks: 3 bond proxies already assigned to first conformer: 11476 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 351 Unusual residues: {'6OU': 2, 'NAG': 3, 'Y01': 7} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'Y01:plan-1': 1, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.08, per 1000 atoms: 0.43 Number of scatterers: 11721 At special positions: 0 Unit cell: (138.446, 137.547, 145.638, 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 89 16.00 P 2 15.00 O 2075 8.00 N 1804 7.00 C 7751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 341 " distance=2.03 Simple disulfide: pdb=" SG CYS A 683 " - pdb=" SG CYS A 686 " distance=2.03 Simple disulfide: pdb=" SG CYS A 906 " - pdb=" SG CYS A 915 " distance=2.04 Simple disulfide: pdb=" SG CYS A1176 " - pdb=" SG CYS A1178 " distance=2.03 Simple disulfide: pdb=" SG CYS A1363 " - pdb=" SG CYS A1384 " distance=2.04 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1742 " 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=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG B 3 " - " NAG B 4 " " NAG B 4 " - " NAG B 5 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2109 " - " ASN A 318 " " NAG A2110 " - " ASN A 283 " " NAG A2111 " - " ASN A 291 " " NAG B 1 " - " ASN A 328 " " NAG E 1 " - " ASN A1365 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 907.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 64.3% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 removed outlier: 4.052A pdb=" N LEU A 21 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 31 removed outlier: 3.981A pdb=" N LYS A 31 " --> pdb=" O MET A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.865A pdb=" N ARG A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.733A pdb=" N CYS A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.947A pdb=" N VAL A 160 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.905A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 232 removed outlier: 4.019A pdb=" N VAL A 223 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.588A pdb=" N LYS A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 removed outlier: 3.772A pdb=" N GLN A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 373 through 386 removed outlier: 4.246A pdb=" N LEU A 377 " --> pdb=" O CYS A 373 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 402 removed outlier: 4.047A pdb=" N PHE A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 433 removed outlier: 3.735A pdb=" N GLN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 705 through 714 Processing helix chain 'A' and resid 718 through 734 removed outlier: 3.811A pdb=" N THR A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 767 removed outlier: 3.606A pdb=" N LEU A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 763 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N MET A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 776 Processing helix chain 'A' and resid 780 through 796 Processing helix chain 'A' and resid 804 through 818 removed outlier: 3.992A pdb=" N PHE A 810 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG A 811 " --> pdb=" O ARG A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 837 Processing helix chain 'A' and resid 839 through 862 removed outlier: 4.021A pdb=" N VAL A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 858 " --> pdb=" O ALA A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 869 removed outlier: 4.299A pdb=" N ARG A 869 " --> pdb=" O SER A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 896 Processing helix chain 'A' and resid 899 through 904 Processing helix chain 'A' and resid 914 through 943 Processing helix chain 'A' and resid 1171 through 1176 removed outlier: 3.915A pdb=" N ARG A1174 " --> pdb=" O GLY A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1188 through 1204 removed outlier: 3.993A pdb=" N TRP A1192 " --> pdb=" O GLY A1188 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS A1204 " --> pdb=" O HIS A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1222 removed outlier: 3.958A pdb=" N GLU A1208 " --> pdb=" O HIS A1204 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1225 No H-bonds generated for 'chain 'A' and resid 1223 through 1225' Processing helix chain 'A' and resid 1226 through 1231 Processing helix chain 'A' and resid 1233 through 1261 removed outlier: 3.789A pdb=" N VAL A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A1261 " --> pdb=" O LYS A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1291 removed outlier: 4.104A pdb=" N LEU A1274 " --> pdb=" O ALA A1270 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A1275 " --> pdb=" O TRP A1271 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A1281 " --> pdb=" O LEU A1277 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A1282 " --> pdb=" O ILE A1278 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A1291 " --> pdb=" O VAL A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1302 Processing helix chain 'A' and resid 1303 through 1316 Proline residue: A1310 - end of helix removed outlier: 4.444A pdb=" N SER A1315 " --> pdb=" O ARG A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1328 Processing helix chain 'A' and resid 1330 through 1357 removed outlier: 3.593A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL A1340 " --> pdb=" O ASN A1336 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A1348 " --> pdb=" O PHE A1344 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A1351 " --> pdb=" O ILE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1387 Processing helix chain 'A' and resid 1404 through 1418 Processing helix chain 'A' and resid 1420 through 1430 removed outlier: 4.078A pdb=" N ILE A1424 " --> pdb=" O GLY A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1445 No H-bonds generated for 'chain 'A' and resid 1443 through 1445' Processing helix chain 'A' and resid 1446 through 1481 removed outlier: 3.883A pdb=" N PHE A1450 " --> pdb=" O MET A1446 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A1459 " --> pdb=" O ILE A1455 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A1460 " --> pdb=" O PHE A1456 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1480 " --> pdb=" O GLN A1476 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A1481 " --> pdb=" O LYS A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1498 removed outlier: 3.749A pdb=" N LYS A1493 " --> pdb=" O GLU A1489 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN A1496 " --> pdb=" O LYS A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1527 removed outlier: 3.743A pdb=" N ASP A1523 " --> pdb=" O GLY A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1545 Processing helix chain 'A' and resid 1553 through 1578 Processing helix chain 'A' and resid 1592 through 1607 removed outlier: 4.033A pdb=" N PHE A1596 " --> pdb=" O ASN A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1612 Processing helix chain 'A' and resid 1620 through 1627 Processing helix chain 'A' and resid 1628 through 1631 Processing helix chain 'A' and resid 1633 through 1638 removed outlier: 3.957A pdb=" N LEU A1636 " --> pdb=" O ILE A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1654 Processing helix chain 'A' and resid 1654 through 1676 removed outlier: 4.341A pdb=" N ASN A1659 " --> pdb=" O PRO A1655 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A1660 " --> pdb=" O ALA A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1708 Processing helix chain 'A' and resid 1713 through 1718 Processing helix chain 'A' and resid 1719 through 1721 No H-bonds generated for 'chain 'A' and resid 1719 through 1721' Processing helix chain 'A' and resid 1744 through 1776 removed outlier: 4.474A pdb=" N LEU A1750 " --> pdb=" O ALA A1746 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A1755 " --> pdb=" O PHE A1751 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1802 removed outlier: 3.866A pdb=" N PHE A1794 " --> pdb=" O ASP A1790 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1818 removed outlier: 4.960A pdb=" N ASP A1816 " --> pdb=" O SER A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1821 No H-bonds generated for 'chain 'A' and resid 1819 through 1821' Processing helix chain 'A' and resid 1831 through 1836 removed outlier: 3.957A pdb=" N ILE A1836 " --> pdb=" O GLN A1832 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1860 removed outlier: 3.581A pdb=" N ARG A1860 " --> pdb=" O ALA A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1882 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 296 Processing sheet with id=AA4, first strand: chain 'A' and resid 1361 through 1365 Processing sheet with id=AA5, first strand: chain 'A' and resid 1808 through 1809 589 hydrogen bonds defined for protein. 1638 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: 1.89 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2454 1.33 - 1.46: 3182 1.46 - 1.58: 6229 1.58 - 1.71: 4 1.71 - 1.84: 145 Bond restraints: 12014 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" N PHE A1571 " pdb=" CA PHE A1571 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.16e+00 bond pdb=" N GLU A 161 " pdb=" CA GLU A 161 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.83e+00 bond pdb=" N ARG A1632 " pdb=" CA ARG A1632 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.39e-02 5.18e+03 5.56e+00 ... (remaining 12009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 16193 4.31 - 8.61: 105 8.61 - 12.92: 11 12.92 - 17.22: 2 17.22 - 21.53: 1 Bond angle restraints: 16312 Sorted by residual: angle pdb=" N THR A 169 " pdb=" CA THR A 169 " pdb=" C THR A 169 " ideal model delta sigma weight residual 111.36 103.82 7.54 1.09e+00 8.42e-01 4.79e+01 angle pdb=" CA MET A1542 " pdb=" CB MET A1542 " pdb=" CG MET A1542 " ideal model delta sigma weight residual 114.10 127.93 -13.83 2.00e+00 2.50e-01 4.78e+01 angle pdb=" CA GLU A1230 " pdb=" CB GLU A1230 " pdb=" CG GLU A1230 " ideal model delta sigma weight residual 114.10 125.52 -11.42 2.00e+00 2.50e-01 3.26e+01 angle pdb=" CA GLU A 737 " pdb=" CB GLU A 737 " pdb=" CG GLU A 737 " ideal model delta sigma weight residual 114.10 124.79 -10.69 2.00e+00 2.50e-01 2.86e+01 angle pdb=" C TRP A 822 " pdb=" N PRO A 823 " pdb=" CD PRO A 823 " ideal model delta sigma weight residual 125.00 103.47 21.53 4.10e+00 5.95e-02 2.76e+01 ... (remaining 16307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.21: 7200 33.21 - 66.42: 370 66.42 - 99.64: 50 99.64 - 132.85: 26 132.85 - 166.06: 1 Dihedral angle restraints: 7647 sinusoidal: 3565 harmonic: 4082 Sorted by residual: dihedral pdb=" CD ARG A1632 " pdb=" NE ARG A1632 " pdb=" CZ ARG A1632 " pdb=" NH1 ARG A1632 " ideal model delta sinusoidal sigma weight residual 0.00 79.49 -79.49 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CB CYS A 280 " pdb=" SG CYS A 280 " pdb=" SG CYS A 335 " pdb=" CB CYS A 335 " ideal model delta sinusoidal sigma weight residual 93.00 169.44 -76.44 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CB CYS A 683 " pdb=" SG CYS A 683 " pdb=" SG CYS A 686 " pdb=" CB CYS A 686 " ideal model delta sinusoidal sigma weight residual 93.00 158.53 -65.53 1 1.00e+01 1.00e-02 5.62e+01 ... (remaining 7644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1559 0.058 - 0.116: 309 0.116 - 0.174: 28 0.174 - 0.232: 6 0.232 - 0.289: 2 Chirality restraints: 1904 Sorted by residual: chirality pdb=" CG LEU A 875 " pdb=" CB LEU A 875 " pdb=" CD1 LEU A 875 " pdb=" CD2 LEU A 875 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA GLU A 747 " pdb=" N GLU A 747 " pdb=" C GLU A 747 " pdb=" CB GLU A 747 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 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 -2.38 -0.02 2.00e-02 2.50e+03 1.10e+00 ... (remaining 1901 not shown) Planarity restraints: 1967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1632 " 1.081 9.50e-02 1.11e+02 4.84e-01 1.42e+02 pdb=" NE ARG A1632 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A1632 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A1632 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A1632 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1638 " 0.947 9.50e-02 1.11e+02 4.24e-01 1.09e+02 pdb=" NE ARG A1638 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A1638 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A1638 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A1638 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 822 " 0.119 5.00e-02 4.00e+02 1.82e-01 5.32e+01 pdb=" N PRO A 823 " -0.315 5.00e-02 4.00e+02 pdb=" CA PRO A 823 " 0.111 5.00e-02 4.00e+02 pdb=" CD PRO A 823 " 0.086 5.00e-02 4.00e+02 ... (remaining 1964 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 89 2.61 - 3.18: 10318 3.18 - 3.75: 16743 3.75 - 4.33: 21538 4.33 - 4.90: 34525 Nonbonded interactions: 83213 Sorted by model distance: nonbonded pdb=" O TYR A 162 " pdb=" OG1 THR A 165 " model vdw 2.031 3.040 nonbonded pdb=" O ALA A 166 " pdb=" OG1 THR A 169 " model vdw 2.080 3.040 nonbonded pdb=" N GLU A1208 " pdb=" OE1 GLU A1208 " model vdw 2.192 3.120 nonbonded pdb=" OG SER A1333 " pdb=" ND2 ASN A1472 " model vdw 2.223 3.120 nonbonded pdb=" O SER A1602 " pdb=" OG1 THR A1606 " model vdw 2.236 3.040 ... (remaining 83208 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 'C' selection = chain 'D' selection = chain 'E' } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.010 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 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 : 0.004 0.075 12033 Z= 0.212 Angle : 0.966 21.531 16362 Z= 0.511 Chirality : 0.046 0.289 1904 Planarity : 0.017 0.484 1962 Dihedral : 20.129 166.062 4986 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.57 % Allowed : 23.13 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.83 (0.23), residues: 1388 helix: 0.34 (0.19), residues: 780 sheet: -3.02 (0.88), residues: 19 loop : -1.67 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1626 TYR 0.033 0.002 TYR A1375 PHE 0.042 0.002 PHE A1791 TRP 0.027 0.002 TRP A 193 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00427 (12014) covalent geometry : angle 0.94434 (16312) SS BOND : bond 0.00473 ( 7) SS BOND : angle 1.99793 ( 14) hydrogen bonds : bond 0.16453 ( 589) hydrogen bonds : angle 5.76457 ( 1638) link_BETA1-4 : bond 0.00678 ( 7) link_BETA1-4 : angle 1.19956 ( 21) link_NAG-ASN : bond 0.00497 ( 5) link_NAG-ASN : angle 6.46798 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 455 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ASN cc_start: 0.7766 (t0) cc_final: 0.7404 (m110) REVERT: A 315 LEU cc_start: 0.7991 (tp) cc_final: 0.7784 (tt) REVERT: A 394 MET cc_start: 0.7713 (tmm) cc_final: 0.7301 (tmm) REVERT: A 748 MET cc_start: 0.5789 (ttm) cc_final: 0.5589 (tmm) REVERT: A 757 THR cc_start: 0.7870 (t) cc_final: 0.7638 (t) REVERT: A 1625 ILE cc_start: 0.8517 (mp) cc_final: 0.8175 (mm) outliers start: 7 outliers final: 1 residues processed: 457 average time/residue: 0.1130 time to fit residues: 72.4153 Evaluate side-chains 322 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 858 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A1354 ASN ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1564 ASN A1765 ASN A1774 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.178752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.151053 restraints weight = 31511.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.155208 restraints weight = 16254.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157864 restraints weight = 10077.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.159618 restraints weight = 7075.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.160787 restraints weight = 5458.258| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4110 r_free = 0.4110 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12033 Z= 0.167 Angle : 0.842 14.899 16362 Z= 0.408 Chirality : 0.046 0.261 1904 Planarity : 0.006 0.064 1962 Dihedral : 16.340 159.986 2347 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.34 % Favored : 93.58 % Rotamer: Outliers : 3.17 % Allowed : 26.06 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.57 (0.23), residues: 1388 helix: 0.68 (0.19), residues: 786 sheet: -1.58 (1.03), residues: 25 loop : -1.84 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 893 TYR 0.027 0.002 TYR A 739 PHE 0.028 0.002 PHE A1791 TRP 0.037 0.002 TRP A 195 HIS 0.002 0.001 HIS A1849 Details of bonding type rmsd covalent geometry : bond 0.00351 (12014) covalent geometry : angle 0.82433 (16312) SS BOND : bond 0.00350 ( 7) SS BOND : angle 1.47614 ( 14) hydrogen bonds : bond 0.05703 ( 589) hydrogen bonds : angle 4.53710 ( 1638) link_BETA1-4 : bond 0.00520 ( 7) link_BETA1-4 : angle 2.15546 ( 21) link_NAG-ASN : bond 0.00564 ( 5) link_NAG-ASN : angle 5.17155 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 340 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8173 (m-80) cc_final: 0.7900 (m-80) REVERT: A 145 CYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8016 (m) REVERT: A 171 GLU cc_start: 0.9051 (pp20) cc_final: 0.8801 (pp20) REVERT: A 219 ARG cc_start: 0.7610 (tpt-90) cc_final: 0.7249 (tpt-90) REVERT: A 275 ASN cc_start: 0.8440 (t0) cc_final: 0.7878 (m110) REVERT: A 315 LEU cc_start: 0.8249 (tp) cc_final: 0.7947 (tt) REVERT: A 394 MET cc_start: 0.8309 (tmm) cc_final: 0.7519 (tmm) REVERT: A 763 GLU cc_start: 0.6830 (pp20) cc_final: 0.6598 (pp20) REVERT: A 810 PHE cc_start: 0.7887 (m-10) cc_final: 0.7256 (m-80) REVERT: A 1199 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.6986 (t80) REVERT: A 1431 SER cc_start: 0.9053 (p) cc_final: 0.8801 (t) REVERT: A 1479 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8533 (mptt) REVERT: A 1552 GLN cc_start: 0.5366 (OUTLIER) cc_final: 0.4618 (tm-30) outliers start: 39 outliers final: 13 residues processed: 367 average time/residue: 0.0963 time to fit residues: 52.1252 Evaluate side-chains 322 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 305 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1722 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN A1463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.175298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.144415 restraints weight = 49086.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.149671 restraints weight = 22085.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.153009 restraints weight = 12719.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.155189 restraints weight = 8414.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156660 restraints weight = 6195.035| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12033 Z= 0.151 Angle : 0.819 14.874 16362 Z= 0.392 Chirality : 0.046 0.247 1904 Planarity : 0.005 0.050 1962 Dihedral : 14.642 145.941 2344 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.34 % Favored : 93.58 % Rotamer: Outliers : 2.84 % Allowed : 27.27 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.69 (0.23), residues: 1388 helix: 0.60 (0.19), residues: 781 sheet: -2.25 (1.08), residues: 15 loop : -1.90 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 383 TYR 0.021 0.002 TYR A1586 PHE 0.051 0.002 PHE A1465 TRP 0.033 0.002 TRP A 195 HIS 0.002 0.000 HIS A 880 Details of bonding type rmsd covalent geometry : bond 0.00333 (12014) covalent geometry : angle 0.80292 (16312) SS BOND : bond 0.00321 ( 7) SS BOND : angle 1.25959 ( 14) hydrogen bonds : bond 0.05175 ( 589) hydrogen bonds : angle 4.43195 ( 1638) link_BETA1-4 : bond 0.00598 ( 7) link_BETA1-4 : angle 2.17944 ( 21) link_NAG-ASN : bond 0.00570 ( 5) link_NAG-ASN : angle 4.74167 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 326 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8182 (m-80) cc_final: 0.7900 (m-80) REVERT: A 145 CYS cc_start: 0.8456 (m) cc_final: 0.8130 (m) REVERT: A 171 GLU cc_start: 0.9023 (pp20) cc_final: 0.8716 (pp20) REVERT: A 219 ARG cc_start: 0.7524 (tpt-90) cc_final: 0.7118 (tpt-90) REVERT: A 275 ASN cc_start: 0.8462 (t0) cc_final: 0.7675 (m110) REVERT: A 315 LEU cc_start: 0.8226 (tp) cc_final: 0.7975 (tt) REVERT: A 346 GLU cc_start: 0.8476 (mp0) cc_final: 0.8182 (pm20) REVERT: A 394 MET cc_start: 0.8341 (tmm) cc_final: 0.7496 (tmm) REVERT: A 810 PHE cc_start: 0.8050 (m-80) cc_final: 0.7432 (m-80) REVERT: A 858 MET cc_start: 0.7505 (ttm) cc_final: 0.7283 (ttt) REVERT: A 1199 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7098 (t80) REVERT: A 1254 MET cc_start: 0.8873 (tpp) cc_final: 0.8023 (tpp) REVERT: A 1296 MET cc_start: 0.6801 (mpp) cc_final: 0.6550 (pmm) REVERT: A 1431 SER cc_start: 0.9139 (p) cc_final: 0.8912 (t) REVERT: A 1488 THR cc_start: 0.8564 (p) cc_final: 0.6502 (p) REVERT: A 1542 MET cc_start: 0.8381 (tpt) cc_final: 0.8103 (tpp) REVERT: A 1552 GLN cc_start: 0.5180 (OUTLIER) cc_final: 0.4630 (tm-30) REVERT: A 1623 ARG cc_start: 0.7697 (tpp80) cc_final: 0.7390 (mmm-85) outliers start: 35 outliers final: 19 residues processed: 348 average time/residue: 0.0894 time to fit residues: 46.2683 Evaluate side-chains 326 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 305 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1463 ASN Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1722 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.0370 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A1354 ASN ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.172615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.144193 restraints weight = 33494.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.148431 restraints weight = 17192.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.151156 restraints weight = 10596.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152944 restraints weight = 7352.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.154141 restraints weight = 5643.724| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12033 Z= 0.159 Angle : 0.806 13.142 16362 Z= 0.385 Chirality : 0.045 0.279 1904 Planarity : 0.005 0.050 1962 Dihedral : 13.442 128.118 2344 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.78 % Favored : 93.08 % Rotamer: Outliers : 3.73 % Allowed : 27.68 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.73 (0.23), residues: 1388 helix: 0.55 (0.19), residues: 783 sheet: -2.21 (1.17), residues: 15 loop : -1.89 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1632 TYR 0.024 0.002 TYR A1375 PHE 0.028 0.002 PHE A1465 TRP 0.032 0.002 TRP A 193 HIS 0.003 0.001 HIS A1849 Details of bonding type rmsd covalent geometry : bond 0.00359 (12014) covalent geometry : angle 0.79075 (16312) SS BOND : bond 0.00294 ( 7) SS BOND : angle 1.20710 ( 14) hydrogen bonds : bond 0.05010 ( 589) hydrogen bonds : angle 4.53085 ( 1638) link_BETA1-4 : bond 0.00552 ( 7) link_BETA1-4 : angle 2.30820 ( 21) link_NAG-ASN : bond 0.00540 ( 5) link_NAG-ASN : angle 4.44940 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 312 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8265 (m-80) cc_final: 0.7991 (m-80) REVERT: A 145 CYS cc_start: 0.8377 (m) cc_final: 0.8113 (m) REVERT: A 171 GLU cc_start: 0.8882 (pp20) cc_final: 0.8649 (pp20) REVERT: A 275 ASN cc_start: 0.8678 (t0) cc_final: 0.8085 (m110) REVERT: A 315 LEU cc_start: 0.8312 (tp) cc_final: 0.8091 (tt) REVERT: A 346 GLU cc_start: 0.8613 (mp0) cc_final: 0.8182 (pm20) REVERT: A 394 MET cc_start: 0.8367 (tmm) cc_final: 0.7694 (tmm) REVERT: A 715 MET cc_start: 0.6505 (mmt) cc_final: 0.6174 (mmm) REVERT: A 810 PHE cc_start: 0.8085 (m-80) cc_final: 0.7382 (m-80) REVERT: A 934 PHE cc_start: 0.9132 (t80) cc_final: 0.8767 (t80) REVERT: A 1199 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7179 (t80) REVERT: A 1261 TYR cc_start: 0.6535 (m-10) cc_final: 0.6213 (m-10) REVERT: A 1265 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7949 (pttp) REVERT: A 1296 MET cc_start: 0.6798 (mpp) cc_final: 0.6559 (pmm) REVERT: A 1316 ARG cc_start: 0.8481 (mmt-90) cc_final: 0.8181 (mmm-85) REVERT: A 1471 ASP cc_start: 0.8990 (m-30) cc_final: 0.8780 (m-30) REVERT: A 1535 MET cc_start: 0.6874 (ptp) cc_final: 0.6218 (mmm) REVERT: A 1552 GLN cc_start: 0.5204 (OUTLIER) cc_final: 0.4715 (tm-30) outliers start: 46 outliers final: 26 residues processed: 339 average time/residue: 0.0974 time to fit residues: 48.2116 Evaluate side-chains 328 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1355 LEU Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1489 GLU Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1722 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 127 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1832 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 = 0.4210 r_free = 0.4210 target = 0.172181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.143736 restraints weight = 33640.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.147919 restraints weight = 17364.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.150637 restraints weight = 10729.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.152438 restraints weight = 7466.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.153627 restraints weight = 5716.446| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12033 Z= 0.144 Angle : 0.809 16.595 16362 Z= 0.380 Chirality : 0.045 0.270 1904 Planarity : 0.005 0.049 1962 Dihedral : 12.764 124.499 2344 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.27 % Favored : 93.58 % Rotamer: Outliers : 3.25 % Allowed : 28.41 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.69 (0.23), residues: 1388 helix: 0.61 (0.19), residues: 782 sheet: -2.23 (1.19), residues: 15 loop : -1.91 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1638 TYR 0.022 0.002 TYR A1375 PHE 0.022 0.001 PHE A1486 TRP 0.031 0.002 TRP A 193 HIS 0.003 0.001 HIS A1849 Details of bonding type rmsd covalent geometry : bond 0.00316 (12014) covalent geometry : angle 0.79450 (16312) SS BOND : bond 0.00274 ( 7) SS BOND : angle 1.08547 ( 14) hydrogen bonds : bond 0.04810 ( 589) hydrogen bonds : angle 4.51696 ( 1638) link_BETA1-4 : bond 0.00662 ( 7) link_BETA1-4 : angle 2.35660 ( 21) link_NAG-ASN : bond 0.00518 ( 5) link_NAG-ASN : angle 4.26344 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8300 (m-80) cc_final: 0.7990 (m-80) REVERT: A 171 GLU cc_start: 0.8893 (pp20) cc_final: 0.8686 (pp20) REVERT: A 227 LEU cc_start: 0.8780 (mt) cc_final: 0.8282 (tt) REVERT: A 275 ASN cc_start: 0.8694 (t0) cc_final: 0.8156 (m110) REVERT: A 315 LEU cc_start: 0.8373 (tp) cc_final: 0.8150 (tt) REVERT: A 346 GLU cc_start: 0.8525 (mp0) cc_final: 0.8112 (pm20) REVERT: A 394 MET cc_start: 0.8311 (tmm) cc_final: 0.7664 (tmm) REVERT: A 715 MET cc_start: 0.6321 (mmt) cc_final: 0.5947 (mmm) REVERT: A 859 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7816 (tp40) REVERT: A 876 LEU cc_start: 0.9239 (mt) cc_final: 0.9014 (mm) REVERT: A 1199 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7172 (t80) REVERT: A 1261 TYR cc_start: 0.6669 (m-10) cc_final: 0.6345 (m-10) REVERT: A 1265 LYS cc_start: 0.8463 (mmtt) cc_final: 0.7968 (pttm) REVERT: A 1316 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.8153 (mmm-85) REVERT: A 1479 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8482 (mtmt) REVERT: A 1535 MET cc_start: 0.6829 (ptp) cc_final: 0.6343 (mmm) REVERT: A 1545 MET cc_start: 0.8644 (tpp) cc_final: 0.8196 (tpp) REVERT: A 1552 GLN cc_start: 0.5265 (OUTLIER) cc_final: 0.4719 (tm-30) REVERT: A 1685 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6835 (mp0) outliers start: 40 outliers final: 29 residues processed: 333 average time/residue: 0.0995 time to fit residues: 49.1309 Evaluate side-chains 329 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1241 TYR Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1489 GLU Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1667 VAL Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1722 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 63 optimal weight: 0.0040 chunk 133 optimal weight: 8.9990 chunk 128 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 0.0370 chunk 126 optimal weight: 0.8980 overall best weight: 0.5270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1832 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 = 0.4241 r_free = 0.4241 target = 0.174660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.146451 restraints weight = 33287.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.150710 restraints weight = 17078.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.153439 restraints weight = 10508.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.155298 restraints weight = 7268.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156478 restraints weight = 5524.700| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12033 Z= 0.134 Angle : 0.793 13.594 16362 Z= 0.371 Chirality : 0.044 0.281 1904 Planarity : 0.005 0.049 1962 Dihedral : 12.002 121.009 2344 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.20 % Favored : 93.66 % Rotamer: Outliers : 2.52 % Allowed : 29.55 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.62 (0.23), residues: 1388 helix: 0.68 (0.19), residues: 785 sheet: -2.17 (1.20), residues: 15 loop : -1.90 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1632 TYR 0.025 0.002 TYR A1755 PHE 0.045 0.001 PHE A1465 TRP 0.028 0.001 TRP A 193 HIS 0.002 0.000 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00290 (12014) covalent geometry : angle 0.77991 (16312) SS BOND : bond 0.00333 ( 7) SS BOND : angle 0.99789 ( 14) hydrogen bonds : bond 0.04417 ( 589) hydrogen bonds : angle 4.39983 ( 1638) link_BETA1-4 : bond 0.00764 ( 7) link_BETA1-4 : angle 2.40495 ( 21) link_NAG-ASN : bond 0.00502 ( 5) link_NAG-ASN : angle 4.02595 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 313 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8326 (m-80) cc_final: 0.8054 (m-80) REVERT: A 275 ASN cc_start: 0.8640 (t0) cc_final: 0.8116 (m110) REVERT: A 315 LEU cc_start: 0.8373 (tp) cc_final: 0.8160 (tt) REVERT: A 346 GLU cc_start: 0.8502 (mp0) cc_final: 0.8066 (pm20) REVERT: A 394 MET cc_start: 0.8281 (tmm) cc_final: 0.7663 (tmm) REVERT: A 421 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8463 (mp10) REVERT: A 715 MET cc_start: 0.6304 (mmt) cc_final: 0.5875 (mmm) REVERT: A 859 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7821 (tp40) REVERT: A 876 LEU cc_start: 0.9274 (mt) cc_final: 0.9050 (mm) REVERT: A 1261 TYR cc_start: 0.6638 (m-10) cc_final: 0.6323 (m-10) REVERT: A 1265 LYS cc_start: 0.8400 (mmtt) cc_final: 0.7929 (pttm) REVERT: A 1479 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8549 (mttp) REVERT: A 1487 MET cc_start: 0.9074 (mmm) cc_final: 0.8526 (mpp) REVERT: A 1535 MET cc_start: 0.6819 (ptp) cc_final: 0.6322 (mmm) REVERT: A 1542 MET cc_start: 0.8036 (tpp) cc_final: 0.7595 (tpp) REVERT: A 1552 GLN cc_start: 0.5326 (OUTLIER) cc_final: 0.4852 (tm-30) REVERT: A 1651 MET cc_start: 0.8492 (mmm) cc_final: 0.8220 (mmm) outliers start: 31 outliers final: 19 residues processed: 332 average time/residue: 0.0993 time to fit residues: 48.7336 Evaluate side-chains 320 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 299 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1349 SER Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1591 TRP Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1704 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1354 ASN ** A1832 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 = 0.4217 r_free = 0.4217 target = 0.172532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.143855 restraints weight = 36214.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.148174 restraints weight = 18185.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150969 restraints weight = 11076.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152825 restraints weight = 7632.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.154060 restraints weight = 5793.630| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12033 Z= 0.142 Angle : 0.820 14.531 16362 Z= 0.385 Chirality : 0.044 0.285 1904 Planarity : 0.005 0.048 1962 Dihedral : 11.592 117.616 2344 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.63 % Favored : 93.22 % Rotamer: Outliers : 2.76 % Allowed : 29.46 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.73 (0.23), residues: 1388 helix: 0.63 (0.19), residues: 801 sheet: -2.18 (1.23), residues: 15 loop : -2.10 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1623 TYR 0.021 0.002 TYR A1495 PHE 0.044 0.001 PHE A1465 TRP 0.026 0.001 TRP A 193 HIS 0.002 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00320 (12014) covalent geometry : angle 0.80712 (16312) SS BOND : bond 0.00264 ( 7) SS BOND : angle 1.02812 ( 14) hydrogen bonds : bond 0.04549 ( 589) hydrogen bonds : angle 4.43577 ( 1638) link_BETA1-4 : bond 0.00678 ( 7) link_BETA1-4 : angle 2.45752 ( 21) link_NAG-ASN : bond 0.00434 ( 5) link_NAG-ASN : angle 3.97591 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 303 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8391 (m-80) cc_final: 0.8075 (m-80) REVERT: A 275 ASN cc_start: 0.8672 (t0) cc_final: 0.8181 (m110) REVERT: A 315 LEU cc_start: 0.8455 (tp) cc_final: 0.8253 (tt) REVERT: A 346 GLU cc_start: 0.8483 (mp0) cc_final: 0.8117 (pm20) REVERT: A 394 MET cc_start: 0.8342 (tmm) cc_final: 0.7679 (tmm) REVERT: A 715 MET cc_start: 0.6367 (mmt) cc_final: 0.5953 (mmm) REVERT: A 876 LEU cc_start: 0.9283 (mt) cc_final: 0.9055 (mm) REVERT: A 1199 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7184 (t80) REVERT: A 1261 TYR cc_start: 0.6747 (m-10) cc_final: 0.6397 (m-10) REVERT: A 1265 LYS cc_start: 0.8483 (mmtt) cc_final: 0.7985 (pttm) REVERT: A 1422 MET cc_start: 0.8938 (mmt) cc_final: 0.8609 (mmp) REVERT: A 1426 TYR cc_start: 0.9007 (m-10) cc_final: 0.8684 (m-80) REVERT: A 1479 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8555 (mttp) REVERT: A 1535 MET cc_start: 0.6916 (ptp) cc_final: 0.6295 (mmm) REVERT: A 1545 MET cc_start: 0.8739 (tpp) cc_final: 0.8117 (tpp) REVERT: A 1546 MET cc_start: 0.8126 (mmp) cc_final: 0.7542 (mmm) REVERT: A 1548 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7713 (tp30) REVERT: A 1552 GLN cc_start: 0.5290 (OUTLIER) cc_final: 0.4769 (tm-30) REVERT: A 1638 ARG cc_start: 0.6684 (ttp80) cc_final: 0.6239 (ttm170) REVERT: A 1651 MET cc_start: 0.8500 (mmm) cc_final: 0.8203 (mmm) outliers start: 34 outliers final: 28 residues processed: 324 average time/residue: 0.0978 time to fit residues: 46.5650 Evaluate side-chains 330 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1241 TYR Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1349 SER Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1468 VAL Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1591 TRP Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1667 VAL Chi-restraints excluded: chain A residue 1704 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 124 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 108 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1832 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 = 0.4231 r_free = 0.4231 target = 0.173963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.143200 restraints weight = 46896.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.148202 restraints weight = 21687.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.151373 restraints weight = 12650.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.153478 restraints weight = 8481.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.154867 restraints weight = 6300.631| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12033 Z= 0.135 Angle : 0.833 15.195 16362 Z= 0.386 Chirality : 0.044 0.288 1904 Planarity : 0.005 0.058 1962 Dihedral : 11.153 116.105 2344 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.63 % Favored : 93.22 % Rotamer: Outliers : 2.19 % Allowed : 30.52 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.69 (0.23), residues: 1388 helix: 0.68 (0.19), residues: 798 sheet: -2.76 (1.09), residues: 10 loop : -2.09 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1623 TYR 0.023 0.002 TYR A1375 PHE 0.026 0.001 PHE A1465 TRP 0.025 0.001 TRP A 193 HIS 0.004 0.001 HIS A 880 Details of bonding type rmsd covalent geometry : bond 0.00298 (12014) covalent geometry : angle 0.82104 (16312) SS BOND : bond 0.00298 ( 7) SS BOND : angle 0.97669 ( 14) hydrogen bonds : bond 0.04376 ( 589) hydrogen bonds : angle 4.41434 ( 1638) link_BETA1-4 : bond 0.00714 ( 7) link_BETA1-4 : angle 2.49048 ( 21) link_NAG-ASN : bond 0.00449 ( 5) link_NAG-ASN : angle 3.81804 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8370 (m-80) cc_final: 0.8052 (m-80) REVERT: A 275 ASN cc_start: 0.8642 (t0) cc_final: 0.8123 (m110) REVERT: A 346 GLU cc_start: 0.8483 (mp0) cc_final: 0.8004 (pm20) REVERT: A 394 MET cc_start: 0.8308 (tmm) cc_final: 0.7654 (tmm) REVERT: A 715 MET cc_start: 0.6235 (mmt) cc_final: 0.5811 (mmm) REVERT: A 725 MET cc_start: 0.8333 (mmm) cc_final: 0.8133 (mmm) REVERT: A 764 MET cc_start: 0.7589 (tpp) cc_final: 0.7113 (tpp) REVERT: A 876 LEU cc_start: 0.9296 (mt) cc_final: 0.9075 (mm) REVERT: A 1261 TYR cc_start: 0.6661 (m-10) cc_final: 0.6316 (m-10) REVERT: A 1265 LYS cc_start: 0.8410 (mmtt) cc_final: 0.7932 (pttm) REVERT: A 1479 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8540 (mttp) REVERT: A 1487 MET cc_start: 0.9084 (mmm) cc_final: 0.8546 (mpp) REVERT: A 1535 MET cc_start: 0.6950 (ptp) cc_final: 0.6363 (mmm) REVERT: A 1545 MET cc_start: 0.8749 (tpp) cc_final: 0.8222 (tpp) REVERT: A 1546 MET cc_start: 0.8048 (mmp) cc_final: 0.7568 (mmm) REVERT: A 1552 GLN cc_start: 0.5377 (OUTLIER) cc_final: 0.4902 (tm-30) REVERT: A 1638 ARG cc_start: 0.6606 (ttp80) cc_final: 0.6173 (ttm170) REVERT: A 1651 MET cc_start: 0.8492 (mmm) cc_final: 0.8195 (mmm) outliers start: 27 outliers final: 20 residues processed: 314 average time/residue: 0.0957 time to fit residues: 44.1304 Evaluate side-chains 303 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 281 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1349 SER Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1591 TRP Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1666 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 57 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN ** A1832 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 = 0.4226 r_free = 0.4226 target = 0.173454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.142462 restraints weight = 49678.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.147574 restraints weight = 22478.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.150847 restraints weight = 12928.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152977 restraints weight = 8594.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.154406 restraints weight = 6360.149| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3986 r_free = 0.3986 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12033 Z= 0.135 Angle : 0.845 15.920 16362 Z= 0.391 Chirality : 0.044 0.275 1904 Planarity : 0.005 0.049 1962 Dihedral : 10.686 113.519 2344 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.42 % Favored : 93.44 % Rotamer: Outliers : 2.11 % Allowed : 30.76 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.66 (0.23), residues: 1388 helix: 0.70 (0.19), residues: 798 sheet: -2.91 (1.12), residues: 10 loop : -2.08 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1623 TYR 0.040 0.002 TYR A1426 PHE 0.027 0.001 PHE A1617 TRP 0.029 0.001 TRP A1421 HIS 0.002 0.000 HIS A1849 Details of bonding type rmsd covalent geometry : bond 0.00300 (12014) covalent geometry : angle 0.83320 (16312) SS BOND : bond 0.00235 ( 7) SS BOND : angle 1.02741 ( 14) hydrogen bonds : bond 0.04344 ( 589) hydrogen bonds : angle 4.43135 ( 1638) link_BETA1-4 : bond 0.00713 ( 7) link_BETA1-4 : angle 2.53692 ( 21) link_NAG-ASN : bond 0.00411 ( 5) link_NAG-ASN : angle 3.73103 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 290 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8442 (m-80) cc_final: 0.8121 (m-80) REVERT: A 275 ASN cc_start: 0.8678 (t0) cc_final: 0.8147 (m110) REVERT: A 346 GLU cc_start: 0.8500 (mp0) cc_final: 0.8018 (pm20) REVERT: A 394 MET cc_start: 0.8317 (tmm) cc_final: 0.7666 (tmm) REVERT: A 715 MET cc_start: 0.6329 (mmt) cc_final: 0.5945 (mmm) REVERT: A 764 MET cc_start: 0.7571 (tpp) cc_final: 0.7077 (tpp) REVERT: A 876 LEU cc_start: 0.9324 (mt) cc_final: 0.9091 (mm) REVERT: A 1261 TYR cc_start: 0.6477 (m-10) cc_final: 0.6130 (m-10) REVERT: A 1265 LYS cc_start: 0.8466 (mmtt) cc_final: 0.7983 (pttm) REVERT: A 1316 ARG cc_start: 0.8615 (mmt180) cc_final: 0.8177 (mmm-85) REVERT: A 1479 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8565 (mttp) REVERT: A 1487 MET cc_start: 0.9074 (mmm) cc_final: 0.8568 (mpp) REVERT: A 1535 MET cc_start: 0.6978 (ptp) cc_final: 0.6376 (mmm) REVERT: A 1545 MET cc_start: 0.8760 (tpp) cc_final: 0.8273 (tpp) REVERT: A 1546 MET cc_start: 0.7978 (mmp) cc_final: 0.7639 (mmm) REVERT: A 1552 GLN cc_start: 0.5404 (OUTLIER) cc_final: 0.4918 (tm-30) REVERT: A 1632 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8021 (ptp90) REVERT: A 1638 ARG cc_start: 0.6565 (ttp80) cc_final: 0.6169 (ttm170) REVERT: A 1651 MET cc_start: 0.8465 (mmm) cc_final: 0.8164 (mmm) REVERT: A 1652 MET cc_start: 0.8394 (mmm) cc_final: 0.7945 (mpp) outliers start: 26 outliers final: 21 residues processed: 309 average time/residue: 0.1020 time to fit residues: 46.9379 Evaluate side-chains 305 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 912 GLN Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1241 TYR Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1591 TRP Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 64 optimal weight: 0.0670 chunk 114 optimal weight: 0.0570 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 129 optimal weight: 0.0000 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 overall best weight: 0.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1832 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 = 0.4247 r_free = 0.4247 target = 0.175323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.142506 restraints weight = 64153.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.148304 restraints weight = 26270.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.151995 restraints weight = 14463.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.154418 restraints weight = 9318.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155997 restraints weight = 6701.264| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4021 r_free = 0.4021 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4021 r_free = 0.4021 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 12033 Z= 0.145 Angle : 0.886 16.156 16362 Z= 0.408 Chirality : 0.044 0.241 1904 Planarity : 0.005 0.046 1962 Dihedral : 10.283 112.304 2344 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.63 % Favored : 93.22 % Rotamer: Outliers : 1.79 % Allowed : 30.84 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.65 (0.23), residues: 1388 helix: 0.69 (0.19), residues: 796 sheet: -2.88 (1.14), residues: 10 loop : -2.03 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1175 TYR 0.039 0.002 TYR A1426 PHE 0.045 0.001 PHE A1465 TRP 0.029 0.001 TRP A1421 HIS 0.002 0.000 HIS A 880 Details of bonding type rmsd covalent geometry : bond 0.00323 (12014) covalent geometry : angle 0.86854 (16312) SS BOND : bond 0.00513 ( 7) SS BOND : angle 3.90309 ( 14) hydrogen bonds : bond 0.04225 ( 589) hydrogen bonds : angle 4.41314 ( 1638) link_BETA1-4 : bond 0.00760 ( 7) link_BETA1-4 : angle 2.60777 ( 21) link_NAG-ASN : bond 0.00464 ( 5) link_NAG-ASN : angle 3.60452 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 289 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8483 (m-80) cc_final: 0.8168 (m-80) REVERT: A 275 ASN cc_start: 0.8617 (t0) cc_final: 0.8110 (m110) REVERT: A 346 GLU cc_start: 0.8424 (mp0) cc_final: 0.7959 (pm20) REVERT: A 394 MET cc_start: 0.8310 (tmm) cc_final: 0.7649 (tmm) REVERT: A 715 MET cc_start: 0.6329 (mmt) cc_final: 0.6117 (mmm) REVERT: A 764 MET cc_start: 0.7530 (tpp) cc_final: 0.7015 (tpp) REVERT: A 876 LEU cc_start: 0.9344 (mt) cc_final: 0.9097 (mm) REVERT: A 1261 TYR cc_start: 0.6450 (m-10) cc_final: 0.6133 (m-10) REVERT: A 1265 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7933 (pttm) REVERT: A 1316 ARG cc_start: 0.8543 (mmt180) cc_final: 0.8093 (mmm-85) REVERT: A 1487 MET cc_start: 0.9062 (mmm) cc_final: 0.8606 (mpp) REVERT: A 1535 MET cc_start: 0.6970 (ptp) cc_final: 0.6382 (mmm) REVERT: A 1545 MET cc_start: 0.8699 (tpp) cc_final: 0.8243 (tpp) REVERT: A 1546 MET cc_start: 0.7929 (mmp) cc_final: 0.7628 (mmm) REVERT: A 1632 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8020 (ptp90) REVERT: A 1638 ARG cc_start: 0.6582 (ttp80) cc_final: 0.6213 (ttm170) REVERT: A 1651 MET cc_start: 0.8425 (mmm) cc_final: 0.8122 (mmm) REVERT: A 1652 MET cc_start: 0.8424 (mmm) cc_final: 0.8002 (mpp) outliers start: 22 outliers final: 19 residues processed: 302 average time/residue: 0.0997 time to fit residues: 45.1618 Evaluate side-chains 310 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1241 TYR Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1591 TRP Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 120 optimal weight: 0.0000 chunk 80 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 30 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1832 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 = 0.4255 r_free = 0.4255 target = 0.175927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.145901 restraints weight = 42859.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150821 restraints weight = 20238.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.153980 restraints weight = 11857.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.156091 restraints weight = 7935.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.157446 restraints weight = 5866.430| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 12033 Z= 0.142 Angle : 0.869 15.922 16362 Z= 0.402 Chirality : 0.044 0.211 1904 Planarity : 0.005 0.046 1962 Dihedral : 9.686 109.570 2344 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.92 % Favored : 92.93 % Rotamer: Outliers : 1.54 % Allowed : 31.17 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.74 (0.23), residues: 1388 helix: 0.64 (0.19), residues: 810 sheet: -2.88 (1.16), residues: 10 loop : -2.17 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1638 TYR 0.035 0.002 TYR A1426 PHE 0.018 0.001 PHE A1486 TRP 0.020 0.001 TRP A 195 HIS 0.001 0.000 HIS A1849 Details of bonding type rmsd covalent geometry : bond 0.00327 (12014) covalent geometry : angle 0.85127 (16312) SS BOND : bond 0.00700 ( 7) SS BOND : angle 3.75310 ( 14) hydrogen bonds : bond 0.04057 ( 589) hydrogen bonds : angle 4.35370 ( 1638) link_BETA1-4 : bond 0.00695 ( 7) link_BETA1-4 : angle 2.72448 ( 21) link_NAG-ASN : bond 0.00380 ( 5) link_NAG-ASN : angle 3.53809 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.34 seconds wall clock time: 49 minutes 53.67 seconds (2993.67 seconds total)