Starting phenix.real_space_refine on Tue Jun 10 13:50:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyk_43663/06_2025/8vyk_43663.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyk_43663/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vyk_43663/06_2025/8vyk_43663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyk_43663/06_2025/8vyk_43663.map" model { file = "/net/cci-nas-00/data/ceres_data/8vyk_43663/06_2025/8vyk_43663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyk_43663/06_2025/8vyk_43663.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 12.41, per 1000 atoms: 1.06 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: 3.03 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.30 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: 3.70 Time building geometry restraints manager: 3.55 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: 1.100 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.950 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.002 TRP A 193 HIS 0.005 0.001 HIS A 118 PHE 0.042 0.002 PHE A1791 TYR 0.033 0.002 TYR A1375 ARG 0.004 0.001 ARG A1626 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 5) link_NAG-ASN : angle 6.46798 ( 15) link_BETA1-4 : bond 0.00678 ( 7) link_BETA1-4 : angle 1.19956 ( 21) hydrogen bonds : bond 0.16453 ( 589) hydrogen bonds : angle 5.76457 ( 1638) SS BOND : bond 0.00473 ( 7) SS BOND : angle 1.99793 ( 14) covalent geometry : bond 0.00427 (12014) covalent geometry : angle 0.94434 (16312) *********************** 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 : 1.300 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: 0.2526 time to fit residues: 160.8718 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 : 1.493 ------------------------------------------------------------------------------- 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 117 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.0570 chunk 126 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.179861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.149258 restraints weight = 48528.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.154488 restraints weight = 21791.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.157795 restraints weight = 12515.972| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4069 r_free = 0.4069 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4069 r_free = 0.4069 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12033 Z= 0.159 Angle : 0.837 14.576 16362 Z= 0.403 Chirality : 0.047 0.275 1904 Planarity : 0.006 0.058 1962 Dihedral : 16.126 159.723 2347 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 3.33 % Allowed : 25.57 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.23), residues: 1388 helix: 0.61 (0.19), residues: 786 sheet: -1.55 (1.02), residues: 25 loop : -1.84 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 195 HIS 0.002 0.001 HIS A1849 PHE 0.028 0.002 PHE A1791 TYR 0.028 0.002 TYR A 739 ARG 0.009 0.001 ARG A 869 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 5) link_NAG-ASN : angle 5.06463 ( 15) link_BETA1-4 : bond 0.00605 ( 7) link_BETA1-4 : angle 2.20294 ( 21) hydrogen bonds : bond 0.05614 ( 589) hydrogen bonds : angle 4.48640 ( 1638) SS BOND : bond 0.00408 ( 7) SS BOND : angle 1.44818 ( 14) covalent geometry : bond 0.00332 (12014) covalent geometry : angle 0.81946 (16312) *********************** 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 385 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 344 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8226 (m-80) cc_final: 0.7959 (m-80) REVERT: A 145 CYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8076 (m) REVERT: A 219 ARG cc_start: 0.7605 (tpt-90) cc_final: 0.5673 (tpt-90) REVERT: A 275 ASN cc_start: 0.8395 (t0) cc_final: 0.7883 (m110) REVERT: A 315 LEU cc_start: 0.8186 (tp) cc_final: 0.7881 (tt) REVERT: A 394 MET cc_start: 0.8339 (tmm) cc_final: 0.7561 (tmm) REVERT: A 763 GLU cc_start: 0.6928 (pp20) cc_final: 0.6701 (pp20) REVERT: A 764 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6983 (tpp) REVERT: A 810 PHE cc_start: 0.7939 (m-80) cc_final: 0.7289 (m-80) REVERT: A 858 MET cc_start: 0.7524 (ttm) cc_final: 0.7318 (ttp) REVERT: A 1199 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.6965 (t80) REVERT: A 1253 GLU cc_start: 0.8835 (tp30) cc_final: 0.8260 (mt-10) REVERT: A 1418 PHE cc_start: 0.8277 (m-80) cc_final: 0.7946 (m-80) REVERT: A 1431 SER cc_start: 0.9089 (p) cc_final: 0.8817 (t) REVERT: A 1552 GLN cc_start: 0.5305 (OUTLIER) cc_final: 0.4599 (tm-30) outliers start: 41 outliers final: 13 residues processed: 373 average time/residue: 0.2416 time to fit residues: 133.4961 Evaluate side-chains 327 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 310 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 764 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 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 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 137 optimal weight: 0.2980 chunk 136 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 89 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN ** A1463 ASN ** 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 = 0.4255 r_free = 0.4255 target = 0.176245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.145762 restraints weight = 46376.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.150951 restraints weight = 21131.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.154246 restraints weight = 12153.891| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- 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 = 0.13 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 = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12033 Z= 0.151 Angle : 0.810 14.491 16362 Z= 0.389 Chirality : 0.045 0.246 1904 Planarity : 0.005 0.049 1962 Dihedral : 14.481 145.128 2344 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.94 % Rotamer: Outliers : 2.84 % Allowed : 27.19 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1388 helix: 0.61 (0.19), residues: 781 sheet: -2.18 (1.07), residues: 15 loop : -1.87 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 193 HIS 0.003 0.000 HIS A 880 PHE 0.029 0.001 PHE A1486 TYR 0.020 0.002 TYR A1495 ARG 0.009 0.001 ARG A1623 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 5) link_NAG-ASN : angle 4.66701 ( 15) link_BETA1-4 : bond 0.00623 ( 7) link_BETA1-4 : angle 2.22021 ( 21) hydrogen bonds : bond 0.05085 ( 589) hydrogen bonds : angle 4.41388 ( 1638) SS BOND : bond 0.00270 ( 7) SS BOND : angle 1.22690 ( 14) covalent geometry : bond 0.00333 (12014) covalent geometry : angle 0.79410 (16312) *********************** 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 360 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 325 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8194 (m-80) cc_final: 0.7911 (m-80) REVERT: A 145 CYS cc_start: 0.8485 (m) cc_final: 0.8161 (m) REVERT: A 195 TRP cc_start: 0.6384 (p90) cc_final: 0.6025 (p90) REVERT: A 219 ARG cc_start: 0.7749 (tpt-90) cc_final: 0.6919 (tpt90) REVERT: A 266 LEU cc_start: 0.8557 (mt) cc_final: 0.8058 (mt) REVERT: A 275 ASN cc_start: 0.8447 (t0) cc_final: 0.7704 (m110) REVERT: A 315 LEU cc_start: 0.8161 (tp) cc_final: 0.7909 (tt) REVERT: A 394 MET cc_start: 0.8363 (tmm) cc_final: 0.7525 (tmm) REVERT: A 810 PHE cc_start: 0.8081 (m-80) cc_final: 0.7445 (m-80) REVERT: A 934 PHE cc_start: 0.9107 (t80) cc_final: 0.8898 (t80) REVERT: A 1199 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7080 (t80) REVERT: A 1296 MET cc_start: 0.6901 (mpp) cc_final: 0.6655 (pmm) REVERT: A 1431 SER cc_start: 0.9131 (p) cc_final: 0.8887 (t) REVERT: A 1488 THR cc_start: 0.8626 (p) cc_final: 0.8142 (p) REVERT: A 1552 GLN cc_start: 0.5077 (OUTLIER) cc_final: 0.4598 (tm-30) REVERT: A 1633 ILE cc_start: 0.8667 (tt) cc_final: 0.8413 (tp) outliers start: 35 outliers final: 21 residues processed: 345 average time/residue: 0.2197 time to fit residues: 112.5144 Evaluate side-chains 324 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 301 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 330 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 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 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 Chi-restraints excluded: chain A residue 1766 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A1354 ASN ** A1541 ASN ** 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 = 0.4211 r_free = 0.4211 target = 0.172297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.143930 restraints weight = 33283.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.148138 restraints weight = 16966.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.150841 restraints weight = 10426.262| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12033 Z= 0.157 Angle : 0.806 13.044 16362 Z= 0.385 Chirality : 0.045 0.283 1904 Planarity : 0.005 0.050 1962 Dihedral : 13.257 127.063 2344 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.07 % Favored : 92.79 % Rotamer: Outliers : 3.57 % Allowed : 27.44 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1388 helix: 0.56 (0.19), residues: 783 sheet: -2.24 (1.17), residues: 15 loop : -1.84 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1421 HIS 0.003 0.001 HIS A1849 PHE 0.037 0.002 PHE A1465 TYR 0.021 0.002 TYR A1755 ARG 0.009 0.001 ARG A1623 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 5) link_NAG-ASN : angle 4.41505 ( 15) link_BETA1-4 : bond 0.00565 ( 7) link_BETA1-4 : angle 2.31049 ( 21) hydrogen bonds : bond 0.04958 ( 589) hydrogen bonds : angle 4.48736 ( 1638) SS BOND : bond 0.00807 ( 7) SS BOND : angle 1.27792 ( 14) covalent geometry : bond 0.00345 (12014) covalent geometry : angle 0.79106 (16312) *********************** 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 359 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 315 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8296 (m-80) cc_final: 0.8018 (m-80) REVERT: A 145 CYS cc_start: 0.8403 (m) cc_final: 0.8134 (m) REVERT: A 195 TRP cc_start: 0.6392 (p90) cc_final: 0.6018 (p90) REVERT: A 227 LEU cc_start: 0.8773 (mt) cc_final: 0.8320 (tt) REVERT: A 275 ASN cc_start: 0.8691 (t0) cc_final: 0.8087 (m110) REVERT: A 315 LEU cc_start: 0.8272 (tp) cc_final: 0.8046 (tt) REVERT: A 322 ASP cc_start: 0.8333 (t0) cc_final: 0.7960 (t0) REVERT: A 346 GLU cc_start: 0.8582 (mp0) cc_final: 0.8182 (pm20) REVERT: A 394 MET cc_start: 0.8402 (tmm) cc_final: 0.7730 (tmm) REVERT: A 794 MET cc_start: 0.6743 (tpp) cc_final: 0.6062 (tmm) REVERT: A 810 PHE cc_start: 0.8104 (m-80) cc_final: 0.7438 (m-80) REVERT: A 812 LEU cc_start: 0.9063 (mt) cc_final: 0.8806 (mt) REVERT: A 859 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7693 (tp40) REVERT: A 934 PHE cc_start: 0.9081 (t80) cc_final: 0.8777 (t80) REVERT: A 1199 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7224 (t80) REVERT: A 1296 MET cc_start: 0.7037 (mpp) cc_final: 0.6825 (pmm) REVERT: A 1479 LYS cc_start: 0.8611 (mttp) cc_final: 0.8342 (mttp) REVERT: A 1488 THR cc_start: 0.8595 (p) cc_final: 0.8083 (p) REVERT: A 1535 MET cc_start: 0.7043 (ptp) cc_final: 0.6782 (mpp) REVERT: A 1552 GLN cc_start: 0.5046 (OUTLIER) cc_final: 0.4582 (tm-30) REVERT: A 1630 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8920 (tp) REVERT: A 1838 MET cc_start: 0.1507 (mtt) cc_final: 0.1118 (ttt) outliers start: 44 outliers final: 25 residues processed: 343 average time/residue: 0.2249 time to fit residues: 113.3291 Evaluate side-chains 325 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU 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 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 858 MET Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1349 SER Chi-restraints excluded: chain A residue 1459 PHE Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 GLN Chi-restraints excluded: chain A residue 1630 ILE 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 75 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.173613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.144591 restraints weight = 36763.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.149034 restraints weight = 18380.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.151882 restraints weight = 11130.866| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12033 Z= 0.141 Angle : 0.805 15.888 16362 Z= 0.380 Chirality : 0.045 0.272 1904 Planarity : 0.005 0.054 1962 Dihedral : 12.585 124.447 2344 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.49 % Favored : 93.37 % Rotamer: Outliers : 3.17 % Allowed : 27.60 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1388 helix: 0.65 (0.19), residues: 785 sheet: -2.25 (1.21), residues: 15 loop : -1.84 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 193 HIS 0.003 0.001 HIS A1849 PHE 0.021 0.001 PHE A1486 TYR 0.025 0.002 TYR A1375 ARG 0.009 0.001 ARG A1638 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 5) link_NAG-ASN : angle 4.19060 ( 15) link_BETA1-4 : bond 0.00669 ( 7) link_BETA1-4 : angle 2.36709 ( 21) hydrogen bonds : bond 0.04724 ( 589) hydrogen bonds : angle 4.41366 ( 1638) SS BOND : bond 0.00343 ( 7) SS BOND : angle 1.03588 ( 14) covalent geometry : bond 0.00309 (12014) covalent geometry : angle 0.79141 (16312) *********************** 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: 39 poor density : 311 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8299 (m-80) cc_final: 0.7989 (m-80) REVERT: A 195 TRP cc_start: 0.6276 (p90) cc_final: 0.5918 (p90) REVERT: A 275 ASN cc_start: 0.8657 (t0) cc_final: 0.8126 (m110) REVERT: A 315 LEU cc_start: 0.8315 (tp) cc_final: 0.8098 (tt) REVERT: A 322 ASP cc_start: 0.8356 (t0) cc_final: 0.8004 (t0) REVERT: A 346 GLU cc_start: 0.8537 (mp0) cc_final: 0.8105 (pm20) REVERT: A 394 MET cc_start: 0.8319 (tmm) cc_final: 0.7668 (tmm) REVERT: A 421 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8635 (mm110) REVERT: A 794 MET cc_start: 0.6779 (tpp) cc_final: 0.6040 (tmm) REVERT: A 810 PHE cc_start: 0.8110 (m-80) cc_final: 0.7463 (m-80) REVERT: A 876 LEU cc_start: 0.9243 (mt) cc_final: 0.9015 (mm) REVERT: A 934 PHE cc_start: 0.9026 (t80) cc_final: 0.8788 (t80) REVERT: A 1199 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7217 (t80) REVERT: A 1265 LYS cc_start: 0.8377 (mmtt) cc_final: 0.7960 (pttm) REVERT: A 1296 MET cc_start: 0.7113 (mpp) cc_final: 0.6902 (pmm) REVERT: A 1425 MET cc_start: 0.8665 (mtp) cc_final: 0.8385 (mtm) REVERT: A 1479 LYS cc_start: 0.8623 (mttp) cc_final: 0.8312 (mttp) REVERT: A 1488 THR cc_start: 0.8587 (p) cc_final: 0.7903 (p) REVERT: A 1489 GLU cc_start: 0.8511 (tp30) cc_final: 0.8231 (tp30) REVERT: A 1535 MET cc_start: 0.7003 (ptp) cc_final: 0.6731 (mpp) REVERT: A 1545 MET cc_start: 0.8617 (tpp) cc_final: 0.8108 (tpp) REVERT: A 1546 MET cc_start: 0.7180 (mmm) cc_final: 0.6891 (mmm) REVERT: A 1552 GLN cc_start: 0.5163 (OUTLIER) cc_final: 0.4636 (tm-30) REVERT: A 1638 ARG cc_start: 0.6803 (ttp80) cc_final: 0.6194 (tpt-90) REVERT: A 1685 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6796 (mp0) REVERT: A 1838 MET cc_start: 0.1468 (mtt) cc_final: 0.1092 (ttt) outliers start: 39 outliers final: 21 residues processed: 331 average time/residue: 0.2186 time to fit residues: 106.0515 Evaluate side-chains 314 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 291 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 726 CYS 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 914 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1314 LEU 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 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 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 26 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.171008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.140689 restraints weight = 47021.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.145533 restraints weight = 21692.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.148637 restraints weight = 12630.456| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12033 Z= 0.151 Angle : 0.820 14.029 16362 Z= 0.387 Chirality : 0.045 0.277 1904 Planarity : 0.005 0.057 1962 Dihedral : 12.063 119.613 2344 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.07 % Favored : 92.79 % Rotamer: Outliers : 2.92 % Allowed : 28.08 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1388 helix: 0.55 (0.19), residues: 799 sheet: -2.21 (1.25), residues: 15 loop : -2.07 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1421 HIS 0.003 0.001 HIS A 738 PHE 0.045 0.002 PHE A1465 TYR 0.027 0.002 TYR A 352 ARG 0.024 0.001 ARG A1623 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 5) link_NAG-ASN : angle 4.15732 ( 15) link_BETA1-4 : bond 0.00595 ( 7) link_BETA1-4 : angle 2.40998 ( 21) hydrogen bonds : bond 0.04747 ( 589) hydrogen bonds : angle 4.48035 ( 1638) SS BOND : bond 0.00300 ( 7) SS BOND : angle 1.13369 ( 14) covalent geometry : bond 0.00337 (12014) covalent geometry : angle 0.80621 (16312) *********************** 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 342 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8384 (m-80) cc_final: 0.8117 (m-80) REVERT: A 195 TRP cc_start: 0.6340 (p90) cc_final: 0.5923 (p90) REVERT: A 275 ASN cc_start: 0.8651 (t0) cc_final: 0.8179 (m110) REVERT: A 322 ASP cc_start: 0.8539 (t0) cc_final: 0.8134 (t0) REVERT: A 346 GLU cc_start: 0.8526 (mp0) cc_final: 0.8156 (pm20) REVERT: A 394 MET cc_start: 0.8383 (tmm) cc_final: 0.7740 (tmm) REVERT: A 810 PHE cc_start: 0.8148 (m-80) cc_final: 0.7419 (m-80) REVERT: A 876 LEU cc_start: 0.9267 (mt) cc_final: 0.9026 (mm) REVERT: A 934 PHE cc_start: 0.9021 (t80) cc_final: 0.8791 (t80) REVERT: A 1199 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7246 (t80) REVERT: A 1216 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8491 (mt) REVERT: A 1265 LYS cc_start: 0.8433 (mmtt) cc_final: 0.7994 (pttm) REVERT: A 1296 MET cc_start: 0.7091 (mpp) cc_final: 0.6874 (pmm) REVERT: A 1425 MET cc_start: 0.8671 (mtp) cc_final: 0.8423 (mtm) REVERT: A 1487 MET cc_start: 0.9074 (mmm) cc_final: 0.8537 (mpp) REVERT: A 1535 MET cc_start: 0.6999 (ptp) cc_final: 0.6754 (mpp) REVERT: A 1545 MET cc_start: 0.8698 (tpp) cc_final: 0.8263 (tpp) REVERT: A 1546 MET cc_start: 0.7428 (mmm) cc_final: 0.7026 (mmm) REVERT: A 1552 GLN cc_start: 0.5340 (OUTLIER) cc_final: 0.4809 (tm-30) REVERT: A 1838 MET cc_start: 0.1483 (mtt) cc_final: 0.1092 (ttt) outliers start: 36 outliers final: 28 residues processed: 328 average time/residue: 0.2031 time to fit residues: 98.3000 Evaluate side-chains 320 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 798 LEU 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 914 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1216 LEU 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 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 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 Chi-restraints excluded: chain A residue 1722 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 69 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.172921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.145006 restraints weight = 33013.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.149200 restraints weight = 16630.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151900 restraints weight = 10150.971| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12033 Z= 0.139 Angle : 0.840 14.555 16362 Z= 0.390 Chirality : 0.045 0.283 1904 Planarity : 0.005 0.046 1962 Dihedral : 11.704 118.239 2344 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.78 % Favored : 93.08 % Rotamer: Outliers : 2.68 % Allowed : 29.22 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1388 helix: 0.57 (0.19), residues: 797 sheet: -2.38 (1.19), residues: 15 loop : -2.03 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 193 HIS 0.002 0.000 HIS A1849 PHE 0.044 0.001 PHE A1465 TYR 0.024 0.002 TYR A1375 ARG 0.009 0.001 ARG A1638 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 5) link_NAG-ASN : angle 3.99272 ( 15) link_BETA1-4 : bond 0.00583 ( 7) link_BETA1-4 : angle 2.41186 ( 21) hydrogen bonds : bond 0.04615 ( 589) hydrogen bonds : angle 4.47051 ( 1638) SS BOND : bond 0.00278 ( 7) SS BOND : angle 0.97833 ( 14) covalent geometry : bond 0.00310 (12014) covalent geometry : angle 0.82780 (16312) *********************** 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 332 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8396 (m-80) cc_final: 0.8083 (m-80) REVERT: A 195 TRP cc_start: 0.6356 (p90) cc_final: 0.5894 (p90) REVERT: A 275 ASN cc_start: 0.8637 (t0) cc_final: 0.8139 (m110) REVERT: A 346 GLU cc_start: 0.8514 (mp0) cc_final: 0.8102 (pm20) REVERT: A 394 MET cc_start: 0.8314 (tmm) cc_final: 0.7710 (tmm) REVERT: A 421 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8758 (mm110) REVERT: A 810 PHE cc_start: 0.8149 (m-80) cc_final: 0.7438 (m-80) REVERT: A 876 LEU cc_start: 0.9268 (mt) cc_final: 0.9042 (mm) REVERT: A 1216 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 1265 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8024 (pttm) REVERT: A 1425 MET cc_start: 0.8702 (mtp) cc_final: 0.8434 (mtm) REVERT: A 1463 ASN cc_start: 0.8390 (t0) cc_final: 0.7924 (t0) REVERT: A 1487 MET cc_start: 0.9027 (mmm) cc_final: 0.8599 (mpp) REVERT: A 1535 MET cc_start: 0.7000 (ptp) cc_final: 0.6763 (mpp) REVERT: A 1545 MET cc_start: 0.8694 (tpp) cc_final: 0.8249 (tpp) REVERT: A 1546 MET cc_start: 0.7122 (mmm) cc_final: 0.6853 (mmm) REVERT: A 1548 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7870 (tp30) REVERT: A 1552 GLN cc_start: 0.5365 (OUTLIER) cc_final: 0.4827 (tm-30) REVERT: A 1638 ARG cc_start: 0.6742 (ttp80) cc_final: 0.6146 (tpt-90) REVERT: A 1838 MET cc_start: 0.1355 (mtt) cc_final: 0.1055 (ttt) outliers start: 33 outliers final: 25 residues processed: 318 average time/residue: 0.2106 time to fit residues: 99.0866 Evaluate side-chains 317 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 363 LEU 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 885 PHE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1216 LEU 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 1327 LEU 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 1599 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1722 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 108 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 35 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1354 ASN ** A1541 ASN ** 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 = 0.171903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.140622 restraints weight = 57017.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.146069 restraints weight = 24202.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.149471 restraints weight = 13483.932| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3934 r_free = 0.3934 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3934 r_free = 0.3934 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12033 Z= 0.143 Angle : 0.839 13.299 16362 Z= 0.389 Chirality : 0.045 0.285 1904 Planarity : 0.005 0.047 1962 Dihedral : 11.379 115.777 2344 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.14 % Favored : 92.72 % Rotamer: Outliers : 2.68 % Allowed : 29.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1388 helix: 0.46 (0.19), residues: 815 sheet: -2.51 (1.20), residues: 15 loop : -2.21 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 193 HIS 0.003 0.001 HIS A1849 PHE 0.034 0.002 PHE A1465 TYR 0.023 0.002 TYR A1375 ARG 0.012 0.001 ARG A1632 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 5) link_NAG-ASN : angle 3.92632 ( 15) link_BETA1-4 : bond 0.00677 ( 7) link_BETA1-4 : angle 2.46151 ( 21) hydrogen bonds : bond 0.04595 ( 589) hydrogen bonds : angle 4.52181 ( 1638) SS BOND : bond 0.00262 ( 7) SS BOND : angle 1.02917 ( 14) covalent geometry : bond 0.00318 (12014) covalent geometry : angle 0.82659 (16312) *********************** 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 321 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 288 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8444 (m-80) cc_final: 0.8128 (m-80) REVERT: A 195 TRP cc_start: 0.6379 (p90) cc_final: 0.5940 (p90) REVERT: A 275 ASN cc_start: 0.8652 (t0) cc_final: 0.8168 (m110) REVERT: A 322 ASP cc_start: 0.8602 (t0) cc_final: 0.8179 (t0) REVERT: A 346 GLU cc_start: 0.8561 (mp0) cc_final: 0.8138 (pm20) REVERT: A 394 MET cc_start: 0.8381 (tmm) cc_final: 0.7733 (tmm) REVERT: A 421 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8489 (mp10) REVERT: A 753 ASN cc_start: 0.8659 (m-40) cc_final: 0.8071 (t0) REVERT: A 810 PHE cc_start: 0.8273 (m-80) cc_final: 0.7627 (m-80) REVERT: A 876 LEU cc_start: 0.9282 (mt) cc_final: 0.9052 (mm) REVERT: A 1199 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7221 (t80) REVERT: A 1216 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8492 (mt) REVERT: A 1265 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8020 (pttm) REVERT: A 1425 MET cc_start: 0.8675 (mtp) cc_final: 0.8419 (mtm) REVERT: A 1463 ASN cc_start: 0.8408 (t0) cc_final: 0.7944 (t0) REVERT: A 1479 LYS cc_start: 0.8501 (mttp) cc_final: 0.8105 (mttp) REVERT: A 1487 MET cc_start: 0.9046 (mmm) cc_final: 0.8635 (mpp) REVERT: A 1535 MET cc_start: 0.7031 (ptp) cc_final: 0.6783 (mpp) REVERT: A 1552 GLN cc_start: 0.5379 (OUTLIER) cc_final: 0.4820 (tm-30) REVERT: A 1838 MET cc_start: 0.1400 (mtt) cc_final: 0.1036 (ttt) outliers start: 33 outliers final: 28 residues processed: 306 average time/residue: 0.2116 time to fit residues: 97.0534 Evaluate side-chains 314 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 885 PHE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1241 TYR Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1355 LEU Chi-restraints excluded: chain A residue 1413 LEU 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 1599 VAL Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1722 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.168226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.140963 restraints weight = 31004.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144801 restraints weight = 16254.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.147284 restraints weight = 10158.001| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3903 r_free = 0.3903 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3903 r_free = 0.3903 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12033 Z= 0.180 Angle : 0.889 13.844 16362 Z= 0.418 Chirality : 0.047 0.276 1904 Planarity : 0.005 0.052 1962 Dihedral : 11.396 113.248 2344 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.79 % Favored : 92.07 % Rotamer: Outliers : 3.00 % Allowed : 29.79 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.23), residues: 1388 helix: 0.33 (0.19), residues: 814 sheet: -2.75 (1.21), residues: 15 loop : -2.33 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 193 HIS 0.003 0.001 HIS A1849 PHE 0.043 0.002 PHE A1465 TYR 0.028 0.002 TYR A1375 ARG 0.008 0.001 ARG A1638 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 5) link_NAG-ASN : angle 4.02152 ( 15) link_BETA1-4 : bond 0.00562 ( 7) link_BETA1-4 : angle 2.51002 ( 21) hydrogen bonds : bond 0.05203 ( 589) hydrogen bonds : angle 4.75776 ( 1638) SS BOND : bond 0.00294 ( 7) SS BOND : angle 1.19608 ( 14) covalent geometry : bond 0.00402 (12014) covalent geometry : angle 0.87704 (16312) *********************** 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 327 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 TRP cc_start: 0.6430 (p90) cc_final: 0.5913 (p90) REVERT: A 275 ASN cc_start: 0.8757 (t0) cc_final: 0.8273 (m110) REVERT: A 346 GLU cc_start: 0.8612 (mp0) cc_final: 0.8257 (pm20) REVERT: A 394 MET cc_start: 0.8406 (tmm) cc_final: 0.7787 (tmm) REVERT: A 738 HIS cc_start: 0.6517 (p90) cc_final: 0.6286 (p90) REVERT: A 753 ASN cc_start: 0.8676 (m-40) cc_final: 0.8063 (t0) REVERT: A 868 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5469 (mt) REVERT: A 1199 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 1216 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8567 (mt) REVERT: A 1265 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8146 (pttm) REVERT: A 1425 MET cc_start: 0.8719 (mtp) cc_final: 0.8476 (mtm) REVERT: A 1479 LYS cc_start: 0.8586 (mttp) cc_final: 0.8156 (mttp) REVERT: A 1487 MET cc_start: 0.9030 (mmm) cc_final: 0.8672 (mpp) REVERT: A 1535 MET cc_start: 0.6991 (ptp) cc_final: 0.6741 (mpp) REVERT: A 1552 GLN cc_start: 0.5832 (OUTLIER) cc_final: 0.5293 (tm-30) REVERT: A 1632 ARG cc_start: 0.8633 (ttp80) cc_final: 0.8193 (ptp90) REVERT: A 1838 MET cc_start: 0.1256 (mtt) cc_final: 0.1019 (ttt) outliers start: 37 outliers final: 27 residues processed: 309 average time/residue: 0.2334 time to fit residues: 107.5066 Evaluate side-chains 313 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR 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 363 LEU Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 787 ILE 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 914 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1241 TYR Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1346 LEU Chi-restraints excluded: chain A residue 1355 LEU 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 Chi-restraints excluded: chain A residue 1704 LEU Chi-restraints excluded: chain A residue 1722 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 41 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.167926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.137885 restraints weight = 47668.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.142709 restraints weight = 21879.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.145763 restraints weight = 12716.454| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 12033 Z= 0.164 Angle : 0.920 15.927 16362 Z= 0.428 Chirality : 0.046 0.246 1904 Planarity : 0.005 0.049 1962 Dihedral : 11.258 112.994 2344 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.79 % Favored : 92.14 % Rotamer: Outliers : 2.84 % Allowed : 30.03 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1388 helix: 0.34 (0.18), residues: 814 sheet: -2.69 (1.21), residues: 15 loop : -2.39 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 193 HIS 0.003 0.001 HIS A1849 PHE 0.029 0.002 PHE A1665 TYR 0.027 0.002 TYR A1375 ARG 0.023 0.001 ARG A 811 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 5) link_NAG-ASN : angle 3.92946 ( 15) link_BETA1-4 : bond 0.00646 ( 7) link_BETA1-4 : angle 2.54215 ( 21) hydrogen bonds : bond 0.05075 ( 589) hydrogen bonds : angle 4.71075 ( 1638) SS BOND : bond 0.00334 ( 7) SS BOND : angle 3.99817 ( 14) covalent geometry : bond 0.00378 (12014) covalent geometry : angle 0.90106 (16312) ********************** 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 321 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 286 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 TRP cc_start: 0.6342 (p90) cc_final: 0.5765 (p90) REVERT: A 275 ASN cc_start: 0.8750 (t0) cc_final: 0.8268 (m110) REVERT: A 346 GLU cc_start: 0.8580 (mp0) cc_final: 0.8265 (pm20) REVERT: A 394 MET cc_start: 0.8403 (tmm) cc_final: 0.7781 (tmm) REVERT: A 753 ASN cc_start: 0.8732 (m-40) cc_final: 0.8521 (p0) REVERT: A 794 MET cc_start: 0.6766 (tpp) cc_final: 0.6456 (ttp) REVERT: A 814 ARG cc_start: 0.8231 (ttm110) cc_final: 0.7939 (tpp80) REVERT: A 868 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5740 (tp) REVERT: A 1199 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7220 (t80) REVERT: A 1216 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8573 (mt) REVERT: A 1425 MET cc_start: 0.8722 (mtp) cc_final: 0.8474 (mtm) REVERT: A 1487 MET cc_start: 0.8987 (mmm) cc_final: 0.8650 (mpp) REVERT: A 1535 MET cc_start: 0.7074 (ptp) cc_final: 0.6821 (mpp) REVERT: A 1552 GLN cc_start: 0.5804 (OUTLIER) cc_final: 0.5202 (tm-30) REVERT: A 1632 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8191 (ptp90) REVERT: A 1691 MET cc_start: 0.7779 (mpp) cc_final: 0.7553 (mpp) REVERT: A 1701 MET cc_start: 0.9025 (tpt) cc_final: 0.8633 (tpp) outliers start: 35 outliers final: 27 residues processed: 307 average time/residue: 0.2425 time to fit residues: 112.0065 Evaluate side-chains 312 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR 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 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 914 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1216 LEU 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 1346 LEU Chi-restraints excluded: chain A residue 1355 LEU 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 Chi-restraints excluded: chain A residue 1696 THR Chi-restraints excluded: chain A residue 1722 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 41 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 101 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN A1269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.170986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.142183 restraints weight = 37363.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.146505 restraints weight = 18669.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.149345 restraints weight = 11327.605| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5612 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= 0.148 Angle : 0.912 16.180 16362 Z= 0.419 Chirality : 0.045 0.206 1904 Planarity : 0.005 0.080 1962 Dihedral : 10.790 111.669 2344 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.35 % Favored : 92.50 % Rotamer: Outliers : 2.19 % Allowed : 30.68 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1388 helix: 0.40 (0.19), residues: 816 sheet: -2.38 (1.24), residues: 15 loop : -2.36 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 193 HIS 0.002 0.000 HIS A1849 PHE 0.044 0.002 PHE A1465 TYR 0.045 0.002 TYR A1426 ARG 0.014 0.001 ARG A 811 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 5) link_NAG-ASN : angle 3.74416 ( 15) link_BETA1-4 : bond 0.00765 ( 7) link_BETA1-4 : angle 2.56229 ( 21) hydrogen bonds : bond 0.04655 ( 589) hydrogen bonds : angle 4.57380 ( 1638) SS BOND : bond 0.00675 ( 7) SS BOND : angle 3.71432 ( 14) covalent geometry : bond 0.00335 (12014) covalent geometry : angle 0.89487 (16312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5463.81 seconds wall clock time: 95 minutes 34.39 seconds (5734.39 seconds total)