Starting phenix.real_space_refine on Thu Jul 2 21:43:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dtd_30851/07_2026/7dtd_30851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtd_30851/07_2026/7dtd_30851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dtd_30851/07_2026/7dtd_30851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtd_30851/07_2026/7dtd_30851.map" model { file = "/net/cci-nas-00/data/ceres_data/7dtd_30851/07_2026/7dtd_30851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtd_30851/07_2026/7dtd_30851.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dtd_30851/07_2026/7dtd_30851.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dtd_30851/07_2026/7dtd_30851.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6739 2.51 5 N 1596 2.21 5 O 1777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10190 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 111, 881 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 111, 881 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 871 Chain: "A" Number of atoms: 9192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 9192 Classifications: {'peptide': 1138} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 1108} Chain breaks: 3 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 95 Unusual residues: {'9Z9': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.18, per 1000 atoms: 0.21 Number of scatterers: 10190 At special positions: 0 Unit cell: (137.238, 139.433, 104.301, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 1777 8.00 N 1596 7.00 C 6739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 131 " distance=2.10 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS A 919 " distance=2.08 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 345 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 351 " distance=2.01 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A 927 " distance=2.03 Simple disulfide: pdb=" SG CYS A 959 " - pdb=" SG CYS A 968 " distance=2.04 Simple disulfide: pdb=" SG CYS A1376 " - pdb=" SG CYS A1396 " distance=2.03 Simple disulfide: pdb=" SG CYS A1741 " - pdb=" SG CYS A1756 " 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 NAG-ASN " NAG A2101 " - " ASN A1403 " " NAG A2102 " - " ASN A1392 " " NAG A2103 " - " ASN A1378 " " NAG A2104 " - " ASN A 338 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 381.1 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 4 sheets defined 68.5% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 136 through 139 Processing helix chain 'A' and resid 117 through 126 removed outlier: 4.094A pdb=" N ALA A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 146 removed outlier: 3.645A pdb=" N SER A 131 " --> pdb=" O HIS A 127 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 177 removed outlier: 3.629A pdb=" N LYS A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 214 through 224 removed outlier: 4.317A pdb=" N THR A 217 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.699A pdb=" N VAL A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 246 removed outlier: 4.165A pdb=" N LYS A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 269 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 368 through 380 Processing helix chain 'A' and resid 383 through 396 removed outlier: 4.013A pdb=" N LEU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 439 removed outlier: 3.593A pdb=" N PHE A 403 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 4.246A pdb=" N VAL A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 787 removed outlier: 3.740A pdb=" N THR A 775 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 819 removed outlier: 4.638A pdb=" N VAL A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 848 removed outlier: 3.949A pdb=" N GLY A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 872 removed outlier: 4.024A pdb=" N LEU A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG A 862 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 864 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 865 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 886 removed outlier: 3.534A pdb=" N ASN A 877 " --> pdb=" O TRP A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 912 Processing helix chain 'A' and resid 914 through 919 Processing helix chain 'A' and resid 920 through 923 Processing helix chain 'A' and resid 936 through 950 Processing helix chain 'A' and resid 953 through 964 removed outlier: 4.005A pdb=" N ASP A 958 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 962 " --> pdb=" O ASP A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 995 removed outlier: 4.175A pdb=" N ASN A 980 " --> pdb=" O MET A 976 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1216 Processing helix chain 'A' and resid 1217 through 1234 removed outlier: 3.860A pdb=" N GLU A1221 " --> pdb=" O HIS A1217 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A1222 " --> pdb=" O ASN A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1245 removed outlier: 3.560A pdb=" N ILE A1242 " --> pdb=" O ASP A1239 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP A1243 " --> pdb=" O ILE A1240 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A1245 " --> pdb=" O ILE A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1281 removed outlier: 3.596A pdb=" N LYS A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A1267 " --> pdb=" O PHE A1263 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR A1276 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N GLN A1277 " --> pdb=" O ALA A1273 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A1278 " --> pdb=" O TYR A1274 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A1281 " --> pdb=" O GLN A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1305 removed outlier: 3.583A pdb=" N GLY A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 Processing helix chain 'A' and resid 1317 through 1327 Proline residue: A1323 - end of helix Processing helix chain 'A' and resid 1330 through 1342 removed outlier: 3.719A pdb=" N VAL A1336 " --> pdb=" O GLY A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1369 removed outlier: 3.667A pdb=" N ILE A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A1361 " --> pdb=" O PHE A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1402 Processing helix chain 'A' and resid 1417 through 1431 Processing helix chain 'A' and resid 1433 through 1443 removed outlier: 3.816A pdb=" N ILE A1437 " --> pdb=" O GLY A1433 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A1443 " --> pdb=" O TYR A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1458 No H-bonds generated for 'chain 'A' and resid 1456 through 1458' Processing helix chain 'A' and resid 1459 through 1470 removed outlier: 3.656A pdb=" N PHE A1463 " --> pdb=" O MET A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1494 removed outlier: 3.693A pdb=" N GLY A1494 " --> pdb=" O LYS A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1515 removed outlier: 3.537A pdb=" N MET A1511 " --> pdb=" O TYR A1507 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A1513 " --> pdb=" O ASN A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1540 removed outlier: 4.002A pdb=" N MET A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A1540 " --> pdb=" O ASP A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1560 removed outlier: 3.560A pdb=" N ASP A1544 " --> pdb=" O ARG A1540 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1560 " --> pdb=" O VAL A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1595 removed outlier: 3.662A pdb=" N ILE A1593 " --> pdb=" O VAL A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1621 removed outlier: 3.724A pdb=" N ILE A1606 " --> pdb=" O ILE A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1639 Processing helix chain 'A' and resid 1642 through 1647 removed outlier: 4.138A pdb=" N ILE A1646 " --> pdb=" O ARG A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1652 removed outlier: 3.954A pdb=" N GLY A1652 " --> pdb=" O LEU A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1692 removed outlier: 3.796A pdb=" N LEU A1659 " --> pdb=" O GLY A1655 " (cutoff:3.500A) Proline residue: A1668 - end of helix removed outlier: 4.049A pdb=" N ASN A1672 " --> pdb=" O PRO A1668 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1722 removed outlier: 3.522A pdb=" N GLN A1719 " --> pdb=" O ILE A1715 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR A1722 " --> pdb=" O PHE A1718 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1734 removed outlier: 3.569A pdb=" N LEU A1729 " --> pdb=" O GLY A1725 " (cutoff:3.500A) Proline residue: A1732 - end of helix Processing helix chain 'A' and resid 1758 through 1793 removed outlier: 4.022A pdb=" N GLU A1787 " --> pdb=" O ALA A1783 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A1790 " --> pdb=" O LEU A1786 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 44 removed outlier: 6.418A pdb=" N ILE B 41 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL B 152 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA B 43 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU B 62 " --> pdb=" O ASN B 86 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN B 86 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 80 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR B 70 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE B 78 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU B 79 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS B 96 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 81 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 40 through 44 removed outlier: 6.418A pdb=" N ILE B 41 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL B 152 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA B 43 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA4, first strand: chain 'A' and resid 1375 through 1378 615 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3072 1.35 - 1.47: 2763 1.47 - 1.60: 4484 1.60 - 1.72: 0 1.72 - 1.85: 127 Bond restraints: 10446 Sorted by residual: bond pdb=" C1 NAG A2103 " pdb=" O5 NAG A2103 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" CA GLU A 853 " pdb=" C GLU A 853 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.34e-02 5.57e+03 2.46e+00 bond pdb=" CA LYS B 77 " pdb=" C LYS B 77 " ideal model delta sigma weight residual 1.520 1.502 0.019 1.22e-02 6.72e+03 2.40e+00 bond pdb=" C04 9Z9 A2105 " pdb=" O72 9Z9 A2105 " ideal model delta sigma weight residual 1.420 1.389 0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" CA LEU B 149 " pdb=" C LEU B 149 " ideal model delta sigma weight residual 1.523 1.505 0.019 1.24e-02 6.50e+03 2.29e+00 ... (remaining 10441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 13648 1.95 - 3.90: 452 3.90 - 5.85: 63 5.85 - 7.80: 14 7.80 - 9.75: 1 Bond angle restraints: 14178 Sorted by residual: angle pdb=" N ARG A 322 " pdb=" CA ARG A 322 " pdb=" C ARG A 322 " ideal model delta sigma weight residual 114.31 107.98 6.33 1.29e+00 6.01e-01 2.40e+01 angle pdb=" N TYR A 826 " pdb=" CA TYR A 826 " pdb=" C TYR A 826 " ideal model delta sigma weight residual 113.02 107.43 5.59 1.20e+00 6.94e-01 2.17e+01 angle pdb=" N VAL A 765 " pdb=" CA VAL A 765 " pdb=" C VAL A 765 " ideal model delta sigma weight residual 106.21 111.13 -4.92 1.07e+00 8.73e-01 2.12e+01 angle pdb=" N HIS A1597 " pdb=" CA HIS A1597 " pdb=" C HIS A1597 " ideal model delta sigma weight residual 114.62 109.40 5.22 1.14e+00 7.69e-01 2.10e+01 angle pdb=" C GLY A 854 " pdb=" N LEU A 855 " pdb=" CA LEU A 855 " ideal model delta sigma weight residual 122.95 115.38 7.57 1.66e+00 3.63e-01 2.08e+01 ... (remaining 14173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 5627 22.99 - 45.99: 400 45.99 - 68.98: 47 68.98 - 91.97: 5 91.97 - 114.97: 1 Dihedral angle restraints: 6080 sinusoidal: 2414 harmonic: 3666 Sorted by residual: dihedral pdb=" CA ARG A1525 " pdb=" C ARG A1525 " pdb=" N PRO A1526 " pdb=" CA PRO A1526 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA VAL A 765 " pdb=" C VAL A 765 " pdb=" N MET A 766 " pdb=" CA MET A 766 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LEU A 186 " pdb=" C LEU A 186 " pdb=" N ARG A 187 " pdb=" CA ARG A 187 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 6077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1259 0.051 - 0.103: 324 0.103 - 0.154: 48 0.154 - 0.206: 11 0.206 - 0.257: 7 Chirality restraints: 1649 Sorted by residual: chirality pdb=" CA AASP B 97 " pdb=" N ASP B 97 " pdb=" C ASP B 97 " pdb=" CB AASP B 97 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU A 186 " pdb=" CB LEU A 186 " pdb=" CD1 LEU A 186 " pdb=" CD2 LEU A 186 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL B 84 " pdb=" N VAL B 84 " pdb=" C VAL B 84 " pdb=" CB VAL B 84 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1646 not shown) Planarity restraints: 1731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 852 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C VAL A 852 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL A 852 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU A 853 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1434 " -0.013 2.00e-02 2.50e+03 1.51e-02 5.70e+00 pdb=" CG TRP A1434 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A1434 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A1434 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A1434 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1434 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1434 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1434 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1434 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A1434 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 357 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO A 358 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " 0.031 5.00e-02 4.00e+02 ... (remaining 1728 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 178 2.67 - 3.22: 10295 3.22 - 3.78: 15220 3.78 - 4.34: 20747 4.34 - 4.90: 33384 Nonbonded interactions: 79824 Sorted by model distance: nonbonded pdb=" O ILE A 318 " pdb=" CG GLN A 319 " model vdw 2.107 3.440 nonbonded pdb=" O THR A 793 " pdb=" N PHE A 796 " model vdw 2.279 3.120 nonbonded pdb=" OD1 ASN A1410 " pdb=" N VAL A1411 " model vdw 2.291 3.120 nonbonded pdb=" O THR A 793 " pdb=" N HIS A 795 " model vdw 2.334 3.120 nonbonded pdb=" O SER A 856 " pdb=" OG SER A 856 " model vdw 2.341 3.040 ... (remaining 79819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.26 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.800 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 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 0.071 10458 Z= 0.231 Angle : 1.123 68.312 14206 Z= 0.641 Chirality : 0.049 0.257 1649 Planarity : 0.004 0.057 1727 Dihedral : 15.105 114.968 3688 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.76 % Favored : 91.35 % Rotamer: Outliers : 2.23 % Allowed : 7.06 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.21), residues: 1242 helix: -1.36 (0.16), residues: 765 sheet: -1.22 (0.56), residues: 75 loop : -3.64 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 100 TYR 0.020 0.001 TYR A 388 PHE 0.015 0.001 PHE A 383 TRP 0.041 0.002 TRP A1434 HIS 0.007 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.23 (10446) covalent geometry : angle 0.84523 / 0.54 (14178) SS BOND : bond 0.03136 / 1.59 ( 8) SS BOND : angle 21.78797 / 12.86 ( 16) hydrogen bonds : bond 0.15957 / 10.39 ( 611) hydrogen bonds : angle 6.10764 / 4.22 ( 1725) link_NAG-ASN : bond 0.03166 / 1.58 ( 4) link_NAG-ASN : angle 3.91528 / 2.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8143 (ttp) cc_final: 0.7909 (ttm) REVERT: A 409 LEU cc_start: 0.8754 (mm) cc_final: 0.8445 (mm) REVERT: A 424 MET cc_start: 0.8268 (tpt) cc_final: 0.7466 (mtm) REVERT: A 815 MET cc_start: 0.8228 (tpp) cc_final: 0.8006 (tpp) REVERT: A 839 ILE cc_start: 0.8471 (mm) cc_final: 0.8263 (mm) REVERT: A 853 GLU cc_start: 0.0716 (OUTLIER) cc_final: 0.0280 (tm-30) REVERT: A 1214 ILE cc_start: 0.8713 (mm) cc_final: 0.8496 (mm) REVERT: A 1219 TRP cc_start: 0.7457 (m-10) cc_final: 0.6982 (m-90) REVERT: A 1226 PHE cc_start: 0.8248 (t80) cc_final: 0.7956 (t80) REVERT: A 1267 MET cc_start: 0.8252 (ttp) cc_final: 0.7622 (tmm) REVERT: A 1277 GLN cc_start: 0.8293 (tp40) cc_final: 0.7265 (mt0) REVERT: A 1608 ASP cc_start: 0.7872 (t70) cc_final: 0.7460 (t70) REVERT: A 1665 MET cc_start: 0.6995 (mmt) cc_final: 0.6411 (mmt) outliers start: 25 outliers final: 12 residues processed: 253 average time/residue: 0.0957 time to fit residues: 35.1784 Evaluate side-chains 181 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1751 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 381 GLN A 416 ASN A 429 GLN A 789 HIS A 933 HIS A1217 HIS A1367 ASN A1375 HIS A1554 ASN A1735 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.162468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.124762 restraints weight = 45925.878| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 4.27 r_work: 0.3437 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10458 Z= 0.195 Angle : 0.732 11.627 14206 Z= 0.374 Chirality : 0.044 0.185 1649 Planarity : 0.005 0.048 1727 Dihedral : 7.510 85.173 1377 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.25 % Favored : 91.51 % Rotamer: Outliers : 3.22 % Allowed : 13.85 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.23), residues: 1242 helix: 0.06 (0.18), residues: 763 sheet: -1.07 (0.52), residues: 87 loop : -2.85 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 216 TYR 0.021 0.002 TYR A 825 PHE 0.018 0.002 PHE A 256 TRP 0.023 0.002 TRP A1434 HIS 0.005 0.001 HIS A1393 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (10446) covalent geometry : angle 0.71985 / 0.37 (14178) SS BOND : bond 0.00595 / 0.24 ( 8) SS BOND : angle 2.39334 / 1.34 ( 16) hydrogen bonds : bond 0.04481 / 2.91 ( 611) hydrogen bonds : angle 4.56192 / 3.18 ( 1725) link_NAG-ASN : bond 0.00412 / 0.20 ( 4) link_NAG-ASN : angle 3.82648 / 2.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.5911 (p90) cc_final: 0.5651 (p90) REVERT: A 253 LEU cc_start: 0.8393 (tt) cc_final: 0.7829 (tp) REVERT: A 377 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8591 (ttt180) REVERT: A 424 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.7789 (mtm) REVERT: A 787 MET cc_start: 0.8962 (mtp) cc_final: 0.8685 (mtp) REVERT: A 918 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7815 (t0) REVERT: A 1214 ILE cc_start: 0.8730 (mm) cc_final: 0.8526 (mm) REVERT: A 1219 TRP cc_start: 0.7665 (m-10) cc_final: 0.7092 (m-90) REVERT: A 1226 PHE cc_start: 0.8531 (t80) cc_final: 0.8255 (t80) REVERT: A 1277 GLN cc_start: 0.8373 (tp40) cc_final: 0.7185 (mt0) REVERT: A 1384 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5965 (mmm-85) REVERT: A 1435 MET cc_start: 0.8328 (mmm) cc_final: 0.8073 (mmp) REVERT: A 1548 MET cc_start: 0.7738 (mtt) cc_final: 0.7104 (tpp) REVERT: A 1608 ASP cc_start: 0.8439 (t70) cc_final: 0.8156 (t70) outliers start: 36 outliers final: 23 residues processed: 197 average time/residue: 0.0948 time to fit residues: 27.3569 Evaluate side-chains 182 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1384 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1616 ILE Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 31 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 HIS A1450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.163860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.124115 restraints weight = 40302.612| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.95 r_work: 0.3463 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10458 Z= 0.147 Angle : 0.668 9.355 14206 Z= 0.341 Chirality : 0.042 0.184 1649 Planarity : 0.004 0.052 1727 Dihedral : 6.581 64.020 1364 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.28 % Favored : 92.40 % Rotamer: Outliers : 4.02 % Allowed : 16.44 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.24), residues: 1242 helix: 0.63 (0.19), residues: 767 sheet: -0.77 (0.53), residues: 87 loop : -2.56 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1402 TYR 0.018 0.002 TYR A 388 PHE 0.024 0.001 PHE A1466 TRP 0.015 0.001 TRP A1434 HIS 0.015 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (10446) covalent geometry : angle 0.65897 / 0.34 (14178) SS BOND : bond 0.00486 / 0.20 ( 8) SS BOND : angle 1.54853 / 0.83 ( 16) hydrogen bonds : bond 0.03915 / 2.52 ( 611) hydrogen bonds : angle 4.26533 / 2.96 ( 1725) link_NAG-ASN : bond 0.00345 / 0.16 ( 4) link_NAG-ASN : angle 3.44225 / 2.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.6062 (p90) cc_final: 0.5813 (p90) REVERT: A 377 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8492 (ttt180) REVERT: A 405 LEU cc_start: 0.9076 (mm) cc_final: 0.8863 (mm) REVERT: A 424 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7652 (mtm) REVERT: A 766 MET cc_start: 0.6579 (tpt) cc_final: 0.6274 (tpt) REVERT: A 787 MET cc_start: 0.8875 (mtp) cc_final: 0.8622 (mtp) REVERT: A 800 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8412 (mm) REVERT: A 918 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7668 (t0) REVERT: A 1214 ILE cc_start: 0.8678 (mm) cc_final: 0.8444 (mm) REVERT: A 1219 TRP cc_start: 0.7627 (m-10) cc_final: 0.7007 (m-90) REVERT: A 1226 PHE cc_start: 0.8567 (t80) cc_final: 0.8289 (t80) REVERT: A 1266 GLU cc_start: 0.8451 (pp20) cc_final: 0.8111 (pp20) REVERT: A 1267 MET cc_start: 0.8535 (tmm) cc_final: 0.8079 (tmm) REVERT: A 1268 LEU cc_start: 0.8761 (mm) cc_final: 0.8015 (mm) REVERT: A 1277 GLN cc_start: 0.8341 (tp40) cc_final: 0.7148 (mt0) REVERT: A 1500 MET cc_start: 0.7711 (mtt) cc_final: 0.7298 (mtp) REVERT: A 1548 MET cc_start: 0.7730 (mtt) cc_final: 0.7049 (tpp) REVERT: A 1608 ASP cc_start: 0.8444 (t70) cc_final: 0.8124 (t70) outliers start: 44 outliers final: 26 residues processed: 202 average time/residue: 0.0763 time to fit residues: 22.8280 Evaluate side-chains 189 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 83 optimal weight: 0.0870 chunk 73 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN A 191 ASN A 272 ASN A 759 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.165482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122361 restraints weight = 53733.880| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 5.46 r_work: 0.3442 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 10458 Z= 0.137 Angle : 0.656 10.466 14206 Z= 0.334 Chirality : 0.041 0.172 1649 Planarity : 0.004 0.050 1727 Dihedral : 6.189 63.428 1361 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.68 % Favored : 92.00 % Rotamer: Outliers : 4.11 % Allowed : 18.23 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1242 helix: 0.98 (0.19), residues: 770 sheet: -0.53 (0.55), residues: 87 loop : -2.51 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1402 TYR 0.016 0.002 TYR A 388 PHE 0.023 0.001 PHE A 200 TRP 0.015 0.001 TRP A1408 HIS 0.006 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10446) covalent geometry : angle 0.64227 / 0.33 (14178) SS BOND : bond 0.00406 / 0.18 ( 8) SS BOND : angle 2.88896 / 1.67 ( 16) hydrogen bonds : bond 0.03615 / 2.33 ( 611) hydrogen bonds : angle 4.11106 / 2.86 ( 1725) link_NAG-ASN : bond 0.00353 / 0.17 ( 4) link_NAG-ASN : angle 3.26414 / 1.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 LEU cc_start: 0.8945 (mm) cc_final: 0.8684 (mm) REVERT: A 424 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7738 (mtm) REVERT: A 766 MET cc_start: 0.6773 (tpt) cc_final: 0.6495 (tpt) REVERT: A 787 MET cc_start: 0.8961 (mtp) cc_final: 0.8746 (mtp) REVERT: A 1214 ILE cc_start: 0.8697 (mm) cc_final: 0.8454 (mm) REVERT: A 1219 TRP cc_start: 0.7686 (m-10) cc_final: 0.7027 (m-90) REVERT: A 1226 PHE cc_start: 0.8532 (t80) cc_final: 0.8264 (t80) REVERT: A 1266 GLU cc_start: 0.8501 (pp20) cc_final: 0.8136 (pp20) REVERT: A 1267 MET cc_start: 0.8562 (tmm) cc_final: 0.8112 (tmm) REVERT: A 1268 LEU cc_start: 0.8749 (mm) cc_final: 0.7992 (mm) REVERT: A 1277 GLN cc_start: 0.8346 (tp40) cc_final: 0.7146 (mt0) REVERT: A 1439 TYR cc_start: 0.8647 (m-10) cc_final: 0.8422 (m-10) REVERT: A 1500 MET cc_start: 0.7807 (mtt) cc_final: 0.7354 (mtp) REVERT: A 1548 MET cc_start: 0.7806 (mtt) cc_final: 0.7132 (tpp) REVERT: A 1608 ASP cc_start: 0.8539 (t70) cc_final: 0.8234 (t70) outliers start: 45 outliers final: 30 residues processed: 212 average time/residue: 0.0751 time to fit residues: 23.9927 Evaluate side-chains 192 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1717 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.164375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121415 restraints weight = 55712.690| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 4.84 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 10458 Z= 0.156 Angle : 0.675 11.310 14206 Z= 0.343 Chirality : 0.042 0.180 1649 Planarity : 0.004 0.052 1727 Dihedral : 5.748 61.005 1357 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.60 % Favored : 92.08 % Rotamer: Outliers : 4.83 % Allowed : 18.95 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1242 helix: 1.02 (0.19), residues: 776 sheet: -0.35 (0.61), residues: 75 loop : -2.36 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1402 TYR 0.018 0.002 TYR A 388 PHE 0.022 0.001 PHE A1466 TRP 0.012 0.001 TRP A1408 HIS 0.004 0.001 HIS A1393 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10446) covalent geometry : angle 0.66161 / 0.34 (14178) SS BOND : bond 0.00548 / 0.26 ( 8) SS BOND : angle 2.89970 / 1.71 ( 16) hydrogen bonds : bond 0.03672 / 2.38 ( 611) hydrogen bonds : angle 4.03459 / 2.79 ( 1725) link_NAG-ASN : bond 0.00332 / 0.16 ( 4) link_NAG-ASN : angle 3.23248 / 1.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7761 (mp) REVERT: A 377 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8453 (ttt180) REVERT: A 409 LEU cc_start: 0.8781 (mm) cc_final: 0.8478 (mm) REVERT: A 424 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7340 (mtm) REVERT: A 766 MET cc_start: 0.6836 (tpt) cc_final: 0.6565 (tpt) REVERT: A 787 MET cc_start: 0.8418 (mtp) cc_final: 0.8197 (mtp) REVERT: A 862 ARG cc_start: 0.7767 (ptm-80) cc_final: 0.7286 (ptm-80) REVERT: A 864 LEU cc_start: 0.8444 (mp) cc_final: 0.8243 (mp) REVERT: A 1214 ILE cc_start: 0.8653 (mm) cc_final: 0.8416 (mm) REVERT: A 1219 TRP cc_start: 0.7692 (m-10) cc_final: 0.6992 (m-90) REVERT: A 1266 GLU cc_start: 0.8172 (pp20) cc_final: 0.7846 (pp20) REVERT: A 1267 MET cc_start: 0.8234 (tmm) cc_final: 0.7842 (tmm) REVERT: A 1268 LEU cc_start: 0.8756 (mm) cc_final: 0.7934 (mm) REVERT: A 1277 GLN cc_start: 0.8266 (tp40) cc_final: 0.7072 (mt0) REVERT: A 1333 MET cc_start: 0.8111 (mtm) cc_final: 0.7527 (mtp) REVERT: A 1500 MET cc_start: 0.6856 (mtt) cc_final: 0.6498 (mtp) REVERT: A 1548 MET cc_start: 0.7358 (mtt) cc_final: 0.7059 (tpp) REVERT: A 1608 ASP cc_start: 0.8341 (t70) cc_final: 0.8058 (t70) REVERT: A 1708 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7500 (mp0) outliers start: 53 outliers final: 34 residues processed: 203 average time/residue: 0.0787 time to fit residues: 24.4704 Evaluate side-chains 196 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1780 MET Chi-restraints excluded: chain A residue 1786 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 0.0010 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 8 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN A 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.162139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.124170 restraints weight = 45457.253| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 4.32 r_work: 0.3432 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10458 Z= 0.178 Angle : 0.677 13.434 14206 Z= 0.343 Chirality : 0.043 0.180 1649 Planarity : 0.004 0.046 1727 Dihedral : 5.652 57.426 1357 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.52 % Favored : 92.16 % Rotamer: Outliers : 5.09 % Allowed : 19.03 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1242 helix: 0.98 (0.19), residues: 778 sheet: -0.42 (0.60), residues: 77 loop : -2.30 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1639 TYR 0.022 0.002 TYR A 388 PHE 0.023 0.001 PHE A1466 TRP 0.013 0.001 TRP A1408 HIS 0.006 0.001 HIS A1393 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (10446) covalent geometry : angle 0.66750 / 0.34 (14178) SS BOND : bond 0.00605 / 0.29 ( 8) SS BOND : angle 1.77402 / 1.01 ( 16) hydrogen bonds : bond 0.03834 / 2.48 ( 611) hydrogen bonds : angle 4.08133 / 2.82 ( 1725) link_NAG-ASN : bond 0.00369 / 0.18 ( 4) link_NAG-ASN : angle 3.46141 / 2.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7728 (mp) REVERT: A 424 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7671 (mtm) REVERT: A 759 HIS cc_start: 0.7565 (m90) cc_final: 0.7361 (m90) REVERT: A 766 MET cc_start: 0.6670 (tpt) cc_final: 0.6423 (tpt) REVERT: A 787 MET cc_start: 0.8964 (mtp) cc_final: 0.8738 (mtp) REVERT: A 800 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 862 ARG cc_start: 0.8028 (ptm-80) cc_final: 0.7682 (ptm-80) REVERT: A 918 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7774 (t0) REVERT: A 1214 ILE cc_start: 0.8744 (mm) cc_final: 0.8494 (mm) REVERT: A 1219 TRP cc_start: 0.7640 (m-10) cc_final: 0.6976 (m-90) REVERT: A 1266 GLU cc_start: 0.8492 (pp20) cc_final: 0.8122 (pp20) REVERT: A 1277 GLN cc_start: 0.8348 (tp40) cc_final: 0.7173 (mt0) REVERT: A 1500 MET cc_start: 0.7635 (mtt) cc_final: 0.7224 (mtp) REVERT: A 1548 MET cc_start: 0.7713 (mtt) cc_final: 0.7110 (tpp) REVERT: A 1608 ASP cc_start: 0.8446 (t70) cc_final: 0.8092 (t70) REVERT: A 1708 GLU cc_start: 0.8564 (mt-10) cc_final: 0.7994 (mp0) outliers start: 56 outliers final: 37 residues processed: 199 average time/residue: 0.0693 time to fit residues: 21.1848 Evaluate side-chains 192 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN B 144 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.163973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.126429 restraints weight = 43445.391| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 4.12 r_work: 0.3472 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10458 Z= 0.138 Angle : 0.662 14.369 14206 Z= 0.331 Chirality : 0.042 0.173 1649 Planarity : 0.004 0.046 1727 Dihedral : 5.475 55.027 1357 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.19 % Favored : 92.48 % Rotamer: Outliers : 4.47 % Allowed : 19.57 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1242 helix: 1.17 (0.19), residues: 777 sheet: -0.40 (0.60), residues: 77 loop : -2.24 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1639 TYR 0.019 0.001 TYR A 388 PHE 0.028 0.001 PHE A 200 TRP 0.013 0.001 TRP A1408 HIS 0.004 0.001 HIS A1393 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (10446) covalent geometry : angle 0.65334 / 0.33 (14178) SS BOND : bond 0.00550 / 0.26 ( 8) SS BOND : angle 1.67939 / 0.96 ( 16) hydrogen bonds : bond 0.03534 / 2.28 ( 611) hydrogen bonds : angle 3.95843 / 2.74 ( 1725) link_NAG-ASN : bond 0.00372 / 0.18 ( 4) link_NAG-ASN : angle 3.34764 / 1.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 424 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7718 (mtm) REVERT: A 787 MET cc_start: 0.8885 (mtp) cc_final: 0.8657 (mtp) REVERT: A 800 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8492 (mm) REVERT: A 808 THR cc_start: 0.9030 (t) cc_final: 0.8803 (t) REVERT: A 822 MET cc_start: 0.7643 (pmm) cc_final: 0.7021 (ptm) REVERT: A 862 ARG cc_start: 0.7873 (ptm-80) cc_final: 0.7629 (ptm-80) REVERT: A 918 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7657 (t0) REVERT: A 1214 ILE cc_start: 0.8678 (mm) cc_final: 0.8414 (mm) REVERT: A 1219 TRP cc_start: 0.7614 (m-10) cc_final: 0.6954 (m-90) REVERT: A 1266 GLU cc_start: 0.8443 (pp20) cc_final: 0.8110 (pp20) REVERT: A 1267 MET cc_start: 0.8554 (tmm) cc_final: 0.8096 (tmm) REVERT: A 1268 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8007 (mm) REVERT: A 1277 GLN cc_start: 0.8340 (tp40) cc_final: 0.7087 (mt0) REVERT: A 1333 MET cc_start: 0.8423 (mtm) cc_final: 0.7887 (mtp) REVERT: A 1500 MET cc_start: 0.7564 (mtt) cc_final: 0.7149 (mtm) REVERT: A 1548 MET cc_start: 0.7681 (mtt) cc_final: 0.7171 (tpp) REVERT: A 1608 ASP cc_start: 0.8415 (t70) cc_final: 0.8072 (t70) REVERT: A 1708 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8038 (mp0) outliers start: 49 outliers final: 32 residues processed: 196 average time/residue: 0.0696 time to fit residues: 20.5282 Evaluate side-chains 194 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.163236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120278 restraints weight = 55045.432| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 5.09 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10458 Z= 0.154 Angle : 0.676 14.612 14206 Z= 0.339 Chirality : 0.042 0.175 1649 Planarity : 0.004 0.044 1727 Dihedral : 5.214 52.185 1354 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.36 % Favored : 92.32 % Rotamer: Outliers : 4.29 % Allowed : 19.75 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1242 helix: 1.28 (0.19), residues: 765 sheet: -0.39 (0.61), residues: 77 loop : -2.11 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1639 TYR 0.020 0.002 TYR A 388 PHE 0.021 0.001 PHE A1466 TRP 0.015 0.001 TRP A1408 HIS 0.005 0.001 HIS A1393 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10446) covalent geometry : angle 0.66774 / 0.34 (14178) SS BOND : bond 0.00579 / 0.26 ( 8) SS BOND : angle 1.68654 / 0.98 ( 16) hydrogen bonds : bond 0.03627 / 2.35 ( 611) hydrogen bonds : angle 3.97987 / 2.75 ( 1725) link_NAG-ASN : bond 0.00353 / 0.17 ( 4) link_NAG-ASN : angle 3.33065 / 1.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7664 (mp) REVERT: A 377 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8396 (ttt180) REVERT: A 424 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7397 (mtm) REVERT: A 800 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8255 (mm) REVERT: A 1214 ILE cc_start: 0.8596 (mm) cc_final: 0.8363 (mm) REVERT: A 1219 TRP cc_start: 0.7618 (m-10) cc_final: 0.6913 (m-90) REVERT: A 1266 GLU cc_start: 0.8184 (pp20) cc_final: 0.7885 (pp20) REVERT: A 1267 MET cc_start: 0.8304 (tmm) cc_final: 0.7900 (tmm) REVERT: A 1277 GLN cc_start: 0.8209 (tp40) cc_final: 0.7869 (tp40) REVERT: A 1400 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6011 (mt) REVERT: A 1500 MET cc_start: 0.6697 (mtt) cc_final: 0.6365 (mtp) REVERT: A 1608 ASP cc_start: 0.8366 (t70) cc_final: 0.8032 (t70) REVERT: A 1708 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7630 (mt-10) outliers start: 47 outliers final: 31 residues processed: 193 average time/residue: 0.0763 time to fit residues: 22.5434 Evaluate side-chains 193 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1384 ARG Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 7 optimal weight: 40.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.164812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.127680 restraints weight = 49134.959| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 4.73 r_work: 0.3460 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10458 Z= 0.129 Angle : 0.673 15.931 14206 Z= 0.332 Chirality : 0.042 0.200 1649 Planarity : 0.004 0.046 1727 Dihedral : 5.087 50.621 1354 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.71 % Favored : 93.05 % Rotamer: Outliers : 3.75 % Allowed : 20.64 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1242 helix: 1.40 (0.19), residues: 765 sheet: -0.37 (0.62), residues: 77 loop : -2.06 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 862 TYR 0.017 0.001 TYR A 388 PHE 0.018 0.001 PHE A1466 TRP 0.016 0.001 TRP A1408 HIS 0.004 0.001 HIS A1393 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (10446) covalent geometry : angle 0.66532 / 0.33 (14178) SS BOND : bond 0.00538 / 0.26 ( 8) SS BOND : angle 1.56379 / 0.92 ( 16) hydrogen bonds : bond 0.03470 / 2.24 ( 611) hydrogen bonds : angle 3.91496 / 2.71 ( 1725) link_NAG-ASN : bond 0.00352 / 0.17 ( 4) link_NAG-ASN : angle 3.18077 / 1.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8640 (p) REVERT: A 278 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7682 (mp) REVERT: A 377 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8598 (ttt180) REVERT: A 424 MET cc_start: 0.8627 (tpt) cc_final: 0.7769 (mtm) REVERT: A 800 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8415 (mm) REVERT: A 1214 ILE cc_start: 0.8686 (mm) cc_final: 0.8422 (mm) REVERT: A 1219 TRP cc_start: 0.7673 (m-10) cc_final: 0.6957 (m-90) REVERT: A 1266 GLU cc_start: 0.8525 (pp20) cc_final: 0.8186 (pp20) REVERT: A 1267 MET cc_start: 0.8575 (tmm) cc_final: 0.8085 (tmm) REVERT: A 1268 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8018 (mm) REVERT: A 1277 GLN cc_start: 0.8305 (tp40) cc_final: 0.7978 (tp40) REVERT: A 1400 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6495 (mt) REVERT: A 1500 MET cc_start: 0.7556 (mtt) cc_final: 0.7151 (mtm) REVERT: A 1608 ASP cc_start: 0.8430 (t70) cc_final: 0.8085 (t70) REVERT: A 1708 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8188 (mt-10) outliers start: 41 outliers final: 26 residues processed: 197 average time/residue: 0.0709 time to fit residues: 21.5584 Evaluate side-chains 191 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1379 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 97 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 119 optimal weight: 0.0970 chunk 109 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN A 267 GLN A 759 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.167301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130112 restraints weight = 51337.573| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 4.89 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10458 Z= 0.121 Angle : 0.658 16.025 14206 Z= 0.326 Chirality : 0.041 0.198 1649 Planarity : 0.004 0.045 1727 Dihedral : 4.915 48.730 1354 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.11 % Favored : 92.64 % Rotamer: Outliers : 3.04 % Allowed : 22.07 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1242 helix: 1.39 (0.19), residues: 776 sheet: -0.26 (0.61), residues: 81 loop : -2.17 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 862 TYR 0.013 0.001 TYR A 388 PHE 0.026 0.001 PHE A1774 TRP 0.020 0.001 TRP A1408 HIS 0.024 0.002 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (10446) covalent geometry : angle 0.65075 / 0.32 (14178) SS BOND : bond 0.00504 / 0.26 ( 8) SS BOND : angle 1.43560 / 0.86 ( 16) hydrogen bonds : bond 0.03300 / 2.14 ( 611) hydrogen bonds : angle 3.86482 / 2.67 ( 1725) link_NAG-ASN : bond 0.00374 / 0.18 ( 4) link_NAG-ASN : angle 2.99642 / 1.78 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 PHE cc_start: 0.7880 (t80) cc_final: 0.7677 (t80) REVERT: A 278 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7610 (mp) REVERT: A 424 MET cc_start: 0.7677 (tpt) cc_final: 0.7372 (mtm) REVERT: A 766 MET cc_start: 0.6549 (tpt) cc_final: 0.6247 (tpp) REVERT: A 767 ASP cc_start: 0.2455 (OUTLIER) cc_final: 0.0621 (t0) REVERT: A 822 MET cc_start: 0.7512 (pmm) cc_final: 0.6572 (ptm) REVERT: A 1214 ILE cc_start: 0.8663 (mm) cc_final: 0.8404 (mm) REVERT: A 1219 TRP cc_start: 0.7670 (m-10) cc_final: 0.6955 (m-90) REVERT: A 1266 GLU cc_start: 0.8158 (pp20) cc_final: 0.7869 (pp20) REVERT: A 1267 MET cc_start: 0.8218 (tmm) cc_final: 0.7860 (tmm) REVERT: A 1268 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.7940 (mm) REVERT: A 1277 GLN cc_start: 0.8222 (tp40) cc_final: 0.7886 (tp40) REVERT: A 1333 MET cc_start: 0.8124 (mtm) cc_final: 0.7525 (mtp) REVERT: A 1500 MET cc_start: 0.6675 (mtt) cc_final: 0.6390 (mtm) REVERT: A 1608 ASP cc_start: 0.8177 (t70) cc_final: 0.7928 (t70) REVERT: A 1708 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7616 (mp0) outliers start: 33 outliers final: 19 residues processed: 191 average time/residue: 0.0692 time to fit residues: 20.5165 Evaluate side-chains 182 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 918 ASP Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 108 optimal weight: 0.0000 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 97 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 0.0870 overall best weight: 0.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN A 759 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.169092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131484 restraints weight = 41943.600| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.99 r_work: 0.3562 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10458 Z= 0.119 Angle : 0.679 19.115 14206 Z= 0.330 Chirality : 0.041 0.195 1649 Planarity : 0.004 0.044 1727 Dihedral : 4.803 47.509 1354 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 2.14 % Allowed : 22.88 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1242 helix: 1.52 (0.19), residues: 776 sheet: -0.16 (0.62), residues: 81 loop : -2.11 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 862 TYR 0.013 0.001 TYR A 388 PHE 0.014 0.001 PHE A1466 TRP 0.013 0.001 TRP A1408 HIS 0.006 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (10446) covalent geometry : angle 0.67234 / 0.33 (14178) SS BOND : bond 0.00538 / 0.27 ( 8) SS BOND : angle 1.59618 / 0.96 ( 16) hydrogen bonds : bond 0.03224 / 2.09 ( 611) hydrogen bonds : angle 3.80869 / 2.64 ( 1725) link_NAG-ASN : bond 0.00351 / 0.17 ( 4) link_NAG-ASN : angle 2.89825 / 1.71 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2598.49 seconds wall clock time: 45 minutes 10.73 seconds (2710.73 seconds total)