Starting phenix.real_space_refine on Mon Jul 28 15:17:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dtd_30851/07_2025/7dtd_30851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtd_30851/07_2025/7dtd_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_2025/7dtd_30851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtd_30851/07_2025/7dtd_30851.map" model { file = "/net/cci-nas-00/data/ceres_data/7dtd_30851/07_2025/7dtd_30851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtd_30851/07_2025/7dtd_30851.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.50, per 1000 atoms: 0.64 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: 2.62 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.04 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: 3.42 Time building geometry restraints manager: 3.14 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: 5770 22.99 - 45.99: 415 45.99 - 68.98: 54 68.98 - 91.97: 7 91.97 - 114.97: 1 Dihedral angle restraints: 6247 sinusoidal: 2581 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 6244 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: 0.950 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 : 15.192 114.968 3855 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.041 0.002 TRP A1434 HIS 0.007 0.001 HIS B 144 PHE 0.015 0.001 PHE A 383 TYR 0.020 0.001 TYR A 388 ARG 0.003 0.000 ARG B 100 Details of bonding type rmsd link_NAG-ASN : bond 0.03166 ( 4) link_NAG-ASN : angle 3.91528 ( 12) hydrogen bonds : bond 0.15957 ( 611) hydrogen bonds : angle 6.10764 ( 1725) SS BOND : bond 0.03136 ( 8) SS BOND : angle 21.78797 ( 16) covalent geometry : bond 0.00414 (10446) covalent geometry : angle 0.84523 (14178) *********************** 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 : 1.235 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: 0.8447 (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: 0.8005 (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: 0.7463 (t70) REVERT: A 1665 MET cc_start: 0.6995 (mmt) cc_final: 0.6412 (mmt) outliers start: 25 outliers final: 12 residues processed: 253 average time/residue: 0.2091 time to fit residues: 75.8142 Evaluate side-chains 180 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 933 HIS A1217 HIS A1367 ASN A1375 HIS A1554 ASN A1735 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.163073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.120086 restraints weight = 58086.683| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 5.26 r_work: 0.3415 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10458 Z= 0.181 Angle : 0.723 11.284 14206 Z= 0.370 Chirality : 0.043 0.179 1649 Planarity : 0.005 0.048 1727 Dihedral : 7.945 65.695 1544 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.08 % Favored : 91.67 % Rotamer: Outliers : 3.22 % Allowed : 13.49 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.24), residues: 1242 helix: 0.09 (0.18), residues: 769 sheet: -1.05 (0.52), residues: 87 loop : -2.82 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1434 HIS 0.005 0.001 HIS A1393 PHE 0.018 0.001 PHE A 256 TYR 0.020 0.002 TYR A 825 ARG 0.005 0.000 ARG A1639 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 4) link_NAG-ASN : angle 3.84136 ( 12) hydrogen bonds : bond 0.04325 ( 611) hydrogen bonds : angle 4.51581 ( 1725) SS BOND : bond 0.00561 ( 8) SS BOND : angle 2.34361 ( 16) covalent geometry : bond 0.00414 (10446) covalent geometry : angle 0.71067 (14178) *********************** 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 208 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.5827 (p90) cc_final: 0.5531 (p90) REVERT: A 253 LEU cc_start: 0.8376 (tt) cc_final: 0.7802 (tp) REVERT: A 377 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8580 (ttt180) REVERT: A 424 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7626 (mtm) REVERT: A 787 MET cc_start: 0.8995 (mtp) cc_final: 0.8737 (mtp) REVERT: A 863 LEU cc_start: 0.9449 (tp) cc_final: 0.9249 (tp) REVERT: A 918 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7826 (t0) REVERT: A 1214 ILE cc_start: 0.8720 (mm) cc_final: 0.8517 (mm) REVERT: A 1219 TRP cc_start: 0.7712 (m-10) cc_final: 0.7127 (m-90) REVERT: A 1226 PHE cc_start: 0.8570 (t80) cc_final: 0.8296 (t80) REVERT: A 1277 GLN cc_start: 0.8362 (tp40) cc_final: 0.7163 (mt0) REVERT: A 1435 MET cc_start: 0.8351 (mmm) cc_final: 0.8094 (mmp) REVERT: A 1500 MET cc_start: 0.7714 (mtt) cc_final: 0.7348 (mtp) REVERT: A 1548 MET cc_start: 0.7759 (mtt) cc_final: 0.7109 (tpp) REVERT: A 1608 ASP cc_start: 0.8508 (t70) cc_final: 0.8229 (t70) outliers start: 36 outliers final: 24 residues processed: 194 average time/residue: 0.2001 time to fit residues: 56.5362 Evaluate side-chains 183 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 1405 THR Chi-restraints excluded: chain A residue 1616 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 1 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 122 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4223 r_free = 0.4223 target = 0.165674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126574 restraints weight = 30426.029| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.52 r_work: 0.3514 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2085 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= 0.131 Angle : 0.645 9.526 14206 Z= 0.331 Chirality : 0.041 0.185 1649 Planarity : 0.004 0.050 1727 Dihedral : 7.045 64.354 1531 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.36 % Favored : 92.40 % Rotamer: Outliers : 3.31 % Allowed : 16.44 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.24), residues: 1242 helix: 0.71 (0.19), residues: 770 sheet: -0.78 (0.52), residues: 87 loop : -2.57 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1408 HIS 0.014 0.001 HIS A 759 PHE 0.021 0.001 PHE A 200 TYR 0.015 0.002 TYR A 317 ARG 0.005 0.000 ARG A1402 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 4) link_NAG-ASN : angle 3.27276 ( 12) hydrogen bonds : bond 0.03759 ( 611) hydrogen bonds : angle 4.19917 ( 1725) SS BOND : bond 0.00610 ( 8) SS BOND : angle 1.52316 ( 16) covalent geometry : bond 0.00284 (10446) covalent geometry : angle 0.63639 (14178) *********************** 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 214 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.6157 (p90) cc_final: 0.5845 (p90) REVERT: A 424 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7680 (mtm) REVERT: A 766 MET cc_start: 0.6468 (tpt) cc_final: 0.6159 (tpt) REVERT: A 787 MET cc_start: 0.8807 (mtp) cc_final: 0.8577 (mtp) REVERT: A 794 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7679 (t0) REVERT: A 800 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8369 (mm) REVERT: A 862 ARG cc_start: 0.7655 (ptm-80) cc_final: 0.7239 (ptm160) REVERT: A 918 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7748 (t0) REVERT: A 1214 ILE cc_start: 0.8678 (mm) cc_final: 0.8442 (mm) REVERT: A 1219 TRP cc_start: 0.7693 (m-10) cc_final: 0.7048 (m-90) REVERT: A 1266 GLU cc_start: 0.8408 (pp20) cc_final: 0.8049 (pp20) REVERT: A 1267 MET cc_start: 0.8513 (tmm) cc_final: 0.8064 (tmm) REVERT: A 1268 LEU cc_start: 0.8739 (mm) cc_final: 0.7977 (mm) REVERT: A 1277 GLN cc_start: 0.8326 (tp40) cc_final: 0.7151 (mt0) REVERT: A 1500 MET cc_start: 0.7593 (mtt) cc_final: 0.7299 (mtp) REVERT: A 1548 MET cc_start: 0.7694 (mtt) cc_final: 0.7078 (tpp) REVERT: A 1608 ASP cc_start: 0.8410 (t70) cc_final: 0.8131 (t70) outliers start: 36 outliers final: 19 residues processed: 202 average time/residue: 0.1885 time to fit residues: 56.7292 Evaluate side-chains 182 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 385 GLU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 800 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 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 1663 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 0.0020 overall best weight: 1.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4203 r_free = 0.4203 target = 0.163848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121486 restraints weight = 55015.283| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 4.94 r_work: 0.3431 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- 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: 22 | |-----------------------------------------------------------------------------| |-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: 22 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2345 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= 0.152 Angle : 0.652 11.807 14206 Z= 0.332 Chirality : 0.042 0.177 1649 Planarity : 0.004 0.056 1727 Dihedral : 6.767 61.756 1528 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.08 % Favored : 91.59 % Rotamer: Outliers : 4.20 % Allowed : 17.69 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1242 helix: 0.90 (0.19), residues: 770 sheet: -0.53 (0.54), residues: 87 loop : -2.51 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1408 HIS 0.004 0.001 HIS A1393 PHE 0.023 0.001 PHE A1466 TYR 0.019 0.002 TYR A 388 ARG 0.007 0.000 ARG A1402 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 4) link_NAG-ASN : angle 3.37825 ( 12) hydrogen bonds : bond 0.03761 ( 611) hydrogen bonds : angle 4.14339 ( 1725) SS BOND : bond 0.00497 ( 8) SS BOND : angle 1.53964 ( 16) covalent geometry : bond 0.00342 (10446) covalent geometry : angle 0.64267 (14178) *********************** 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 216 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8077 (mmt) cc_final: 0.7868 (mmm) REVERT: A 377 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8545 (ttt180) REVERT: A 409 LEU cc_start: 0.8947 (mm) cc_final: 0.8695 (mm) REVERT: A 424 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7709 (mtm) REVERT: A 766 MET cc_start: 0.6751 (tpt) cc_final: 0.6479 (tpt) REVERT: A 787 MET cc_start: 0.8927 (mtp) cc_final: 0.8710 (mtp) REVERT: A 862 ARG cc_start: 0.7708 (ptm-80) cc_final: 0.7379 (ptm160) REVERT: A 1214 ILE cc_start: 0.8699 (mm) cc_final: 0.8453 (mm) REVERT: A 1219 TRP cc_start: 0.7695 (m-10) cc_final: 0.7016 (m-90) REVERT: A 1266 GLU cc_start: 0.8478 (pp20) cc_final: 0.8129 (pp20) REVERT: A 1267 MET cc_start: 0.8563 (tmm) cc_final: 0.8087 (tmm) REVERT: A 1268 LEU cc_start: 0.8740 (mm) cc_final: 0.7985 (mm) REVERT: A 1277 GLN cc_start: 0.8349 (tp40) cc_final: 0.7148 (mt0) REVERT: A 1500 MET cc_start: 0.7778 (mtt) cc_final: 0.7526 (mtp) REVERT: A 1548 MET cc_start: 0.7721 (mtt) cc_final: 0.7146 (tpp) REVERT: A 1608 ASP cc_start: 0.8571 (t70) cc_final: 0.8268 (t70) REVERT: A 1628 TYR cc_start: 0.4638 (m-80) cc_final: 0.4399 (m-10) outliers start: 46 outliers final: 29 residues processed: 198 average time/residue: 0.1883 time to fit residues: 55.7293 Evaluate side-chains 187 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 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 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 808 THR 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 Chi-restraints excluded: chain A residue 1780 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN A 789 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.163385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126981 restraints weight = 45514.936| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 4.56 r_work: 0.3449 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 10458 Z= 0.164 Angle : 0.674 11.964 14206 Z= 0.342 Chirality : 0.042 0.179 1649 Planarity : 0.004 0.051 1727 Dihedral : 6.572 60.113 1526 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.28 % Favored : 92.40 % Rotamer: Outliers : 4.65 % Allowed : 19.21 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1242 helix: 0.97 (0.19), residues: 776 sheet: -0.19 (0.62), residues: 75 loop : -2.49 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1408 HIS 0.004 0.001 HIS A1393 PHE 0.023 0.001 PHE A1466 TYR 0.020 0.002 TYR A 388 ARG 0.004 0.000 ARG A1402 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 4) link_NAG-ASN : angle 3.45664 ( 12) hydrogen bonds : bond 0.03736 ( 611) hydrogen bonds : angle 4.06124 ( 1725) SS BOND : bond 0.00595 ( 8) SS BOND : angle 2.77805 ( 16) covalent geometry : bond 0.00378 (10446) covalent geometry : angle 0.66077 (14178) *********************** 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 221 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8095 (mmt) cc_final: 0.7636 (mmm) REVERT: A 278 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7931 (mp) REVERT: A 409 LEU cc_start: 0.8924 (mm) cc_final: 0.8668 (mm) REVERT: A 424 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7617 (mtm) REVERT: A 787 MET cc_start: 0.8950 (mtp) cc_final: 0.8731 (mtp) REVERT: A 1214 ILE cc_start: 0.8717 (mm) cc_final: 0.8463 (mm) REVERT: A 1219 TRP cc_start: 0.7640 (m-10) cc_final: 0.6998 (m-90) REVERT: A 1266 GLU cc_start: 0.8463 (pp20) cc_final: 0.8139 (pp20) REVERT: A 1277 GLN cc_start: 0.8322 (tp40) cc_final: 0.7154 (mt0) REVERT: A 1333 MET cc_start: 0.8420 (mtm) cc_final: 0.7880 (mtp) REVERT: A 1500 MET cc_start: 0.7587 (mtt) cc_final: 0.7327 (mtp) REVERT: A 1548 MET cc_start: 0.7730 (mtt) cc_final: 0.7126 (tpp) REVERT: A 1608 ASP cc_start: 0.8491 (t70) cc_final: 0.8166 (t70) REVERT: A 1628 TYR cc_start: 0.4747 (m-80) cc_final: 0.4528 (m-10) REVERT: A 1708 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8032 (mp0) outliers start: 51 outliers final: 36 residues processed: 200 average time/residue: 0.1913 time to fit residues: 57.6426 Evaluate side-chains 198 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 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 793 THR Chi-restraints excluded: chain A residue 808 THR 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 969 LEU 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 1384 ARG 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 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 110 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 102 optimal weight: 0.7980 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN A 359 ASN A1577 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.160398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123098 restraints weight = 51267.353| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 4.94 r_work: 0.3382 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 10458 Z= 0.254 Angle : 0.764 12.913 14206 Z= 0.386 Chirality : 0.046 0.199 1649 Planarity : 0.004 0.046 1727 Dihedral : 6.705 58.499 1524 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.57 % Favored : 91.11 % Rotamer: Outliers : 5.99 % Allowed : 19.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1242 helix: 0.72 (0.18), residues: 782 sheet: -0.30 (0.60), residues: 75 loop : -2.47 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1408 HIS 0.007 0.001 HIS A1393 PHE 0.026 0.002 PHE A 200 TYR 0.027 0.002 TYR A 388 ARG 0.004 0.000 ARG A 862 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 4) link_NAG-ASN : angle 3.86534 ( 12) hydrogen bonds : bond 0.04170 ( 611) hydrogen bonds : angle 4.24464 ( 1725) SS BOND : bond 0.00610 ( 8) SS BOND : angle 3.58404 ( 16) covalent geometry : bond 0.00602 (10446) covalent geometry : angle 0.74703 (14178) *********************** 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 225 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 159 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7761 (mtm) REVERT: A 759 HIS cc_start: 0.7600 (m90) cc_final: 0.7339 (m90) REVERT: A 766 MET cc_start: 0.6663 (tpt) cc_final: 0.6329 (tpt) REVERT: A 787 MET cc_start: 0.9034 (mtp) cc_final: 0.8808 (mtp) REVERT: A 918 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7917 (t0) REVERT: A 1214 ILE cc_start: 0.8728 (mm) cc_final: 0.8473 (mm) REVERT: A 1219 TRP cc_start: 0.7673 (m-10) cc_final: 0.7003 (m-90) REVERT: A 1266 GLU cc_start: 0.8505 (pp20) cc_final: 0.8202 (pp20) REVERT: A 1267 MET cc_start: 0.8560 (tmm) cc_final: 0.8096 (tmm) REVERT: A 1277 GLN cc_start: 0.8351 (tp40) cc_final: 0.7188 (mt0) REVERT: A 1548 MET cc_start: 0.7810 (mtt) cc_final: 0.7213 (tpp) REVERT: A 1608 ASP cc_start: 0.8544 (t70) cc_final: 0.8175 (t70) REVERT: A 1708 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8265 (mt-10) outliers start: 66 outliers final: 41 residues processed: 202 average time/residue: 0.2869 time to fit residues: 89.7534 Evaluate side-chains 196 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 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 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 808 THR 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 971 VAL Chi-restraints excluded: chain A residue 1224 ILE 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 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 1384 ARG 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 57 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4200 r_free = 0.4200 target = 0.163364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126653 restraints weight = 43647.830| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 4.26 r_work: 0.3462 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 10458 Z= 0.152 Angle : 0.680 13.520 14206 Z= 0.343 Chirality : 0.042 0.183 1649 Planarity : 0.004 0.047 1727 Dihedral : 6.348 59.075 1524 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.76 % Favored : 91.92 % Rotamer: Outliers : 5.09 % Allowed : 19.48 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1242 helix: 1.15 (0.19), residues: 759 sheet: -0.43 (0.60), residues: 77 loop : -2.26 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1434 HIS 0.004 0.001 HIS A1393 PHE 0.020 0.001 PHE A1466 TYR 0.018 0.002 TYR A 388 ARG 0.002 0.000 ARG A1639 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 4) link_NAG-ASN : angle 3.63367 ( 12) hydrogen bonds : bond 0.03642 ( 611) hydrogen bonds : angle 4.02524 ( 1725) SS BOND : bond 0.00610 ( 8) SS BOND : angle 2.68745 ( 16) covalent geometry : bond 0.00350 (10446) covalent geometry : angle 0.66674 (14178) *********************** 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 222 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8151 (mmt) cc_final: 0.7697 (mmm) REVERT: A 409 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8683 (mm) REVERT: A 424 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7651 (mtm) REVERT: A 766 MET cc_start: 0.6657 (tpt) cc_final: 0.6357 (tpt) REVERT: A 787 MET cc_start: 0.8897 (mtp) cc_final: 0.8681 (mtp) REVERT: A 804 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7311 (t0) REVERT: A 918 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7742 (t0) REVERT: A 1214 ILE cc_start: 0.8686 (mm) cc_final: 0.8425 (mm) REVERT: A 1219 TRP cc_start: 0.7618 (m-10) cc_final: 0.6954 (m-90) REVERT: A 1266 GLU cc_start: 0.8460 (pp20) cc_final: 0.8166 (pp20) REVERT: A 1267 MET cc_start: 0.8535 (tmm) cc_final: 0.8041 (tmm) REVERT: A 1277 GLN cc_start: 0.8329 (tp40) cc_final: 0.7082 (mt0) REVERT: A 1333 MET cc_start: 0.8470 (mtm) cc_final: 0.7945 (mtp) REVERT: A 1500 MET cc_start: 0.7574 (mtt) cc_final: 0.7360 (mtp) REVERT: A 1608 ASP cc_start: 0.8412 (t70) cc_final: 0.8054 (t70) REVERT: A 1708 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8163 (mt-10) outliers start: 56 outliers final: 32 residues processed: 201 average time/residue: 0.2044 time to fit residues: 61.3310 Evaluate side-chains 190 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 169 SER 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 377 ARG Chi-restraints excluded: chain A residue 409 LEU 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 804 ASN Chi-restraints excluded: chain A residue 808 THR 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 971 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 1379 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1563 ASP Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain A residue 1780 MET Chi-restraints excluded: chain A residue 1786 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 40.0000 chunk 77 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.161302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123579 restraints weight = 50585.578| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.87 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10458 Z= 0.190 Angle : 0.714 15.242 14206 Z= 0.359 Chirality : 0.044 0.196 1649 Planarity : 0.004 0.045 1727 Dihedral : 6.252 59.519 1521 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.84 % Favored : 91.84 % Rotamer: Outliers : 4.56 % Allowed : 19.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1242 helix: 1.11 (0.19), residues: 764 sheet: -0.53 (0.60), residues: 77 loop : -2.28 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1408 HIS 0.006 0.001 HIS A1393 PHE 0.028 0.002 PHE A 200 TYR 0.023 0.002 TYR A 388 ARG 0.012 0.000 ARG A 862 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 4) link_NAG-ASN : angle 3.65622 ( 12) hydrogen bonds : bond 0.03918 ( 611) hydrogen bonds : angle 4.11769 ( 1725) SS BOND : bond 0.00599 ( 8) SS BOND : angle 2.37648 ( 16) covalent geometry : bond 0.00443 (10446) covalent geometry : angle 0.70265 (14178) *********************** 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 205 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7701 (mp) REVERT: A 409 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8374 (mm) REVERT: A 424 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7421 (mtm) REVERT: A 766 MET cc_start: 0.6659 (tpt) cc_final: 0.6334 (tpt) REVERT: A 804 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.6856 (t0) REVERT: A 1214 ILE cc_start: 0.8719 (mm) cc_final: 0.8469 (mm) REVERT: A 1219 TRP cc_start: 0.7647 (m-10) cc_final: 0.6963 (m-90) REVERT: A 1266 GLU cc_start: 0.8146 (pp20) cc_final: 0.7941 (pp20) REVERT: A 1267 MET cc_start: 0.8213 (tmm) cc_final: 0.7812 (tmm) REVERT: A 1277 GLN cc_start: 0.8231 (tp40) cc_final: 0.7891 (tp40) REVERT: A 1333 MET cc_start: 0.8341 (mtm) cc_final: 0.7726 (mtp) REVERT: A 1400 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6237 (mt) REVERT: A 1608 ASP cc_start: 0.8171 (t70) cc_final: 0.7864 (t70) REVERT: A 1708 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7568 (mt-10) outliers start: 50 outliers final: 36 residues processed: 187 average time/residue: 0.1887 time to fit residues: 53.3445 Evaluate side-chains 191 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 377 ARG Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 760 VAL 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 804 ASN 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 971 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 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 1563 ASP Chi-restraints excluded: chain A residue 1587 GLU 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 1760 SER 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 2 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 70.0000 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.160828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118176 restraints weight = 55726.193| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 5.06 r_work: 0.3392 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10458 Z= 0.199 Angle : 0.718 14.969 14206 Z= 0.362 Chirality : 0.044 0.196 1649 Planarity : 0.004 0.046 1727 Dihedral : 6.324 59.000 1521 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.16 % Favored : 91.51 % Rotamer: Outliers : 4.74 % Allowed : 19.75 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1242 helix: 1.06 (0.18), residues: 768 sheet: -0.40 (0.60), residues: 75 loop : -2.27 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1408 HIS 0.006 0.001 HIS A1393 PHE 0.023 0.002 PHE A1466 TYR 0.025 0.002 TYR A 388 ARG 0.008 0.000 ARG A 862 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 4) link_NAG-ASN : angle 3.67198 ( 12) hydrogen bonds : bond 0.03966 ( 611) hydrogen bonds : angle 4.15660 ( 1725) SS BOND : bond 0.00647 ( 8) SS BOND : angle 1.95559 ( 16) covalent geometry : bond 0.00466 (10446) covalent geometry : angle 0.70733 (14178) *********************** 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 209 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 157 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 409 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8652 (mm) REVERT: A 424 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.7703 (mtm) REVERT: A 766 MET cc_start: 0.6749 (tpt) cc_final: 0.6460 (tpt) REVERT: A 804 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7484 (t0) REVERT: A 822 MET cc_start: 0.7543 (pmm) cc_final: 0.6430 (ptm) REVERT: A 1214 ILE cc_start: 0.8746 (mm) cc_final: 0.8496 (mm) REVERT: A 1219 TRP cc_start: 0.7674 (m-10) cc_final: 0.6971 (m-90) REVERT: A 1266 GLU cc_start: 0.8495 (pp20) cc_final: 0.8291 (pp20) REVERT: A 1277 GLN cc_start: 0.8272 (tp40) cc_final: 0.7906 (tp40) REVERT: A 1333 MET cc_start: 0.8581 (mtm) cc_final: 0.8005 (mtp) REVERT: A 1384 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.5738 (mtm-85) REVERT: A 1400 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6567 (mt) REVERT: A 1608 ASP cc_start: 0.8468 (t70) cc_final: 0.8156 (t70) REVERT: A 1708 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8272 (mt-10) outliers start: 52 outliers final: 37 residues processed: 193 average time/residue: 0.1803 time to fit residues: 52.3121 Evaluate side-chains 194 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 229 VAL 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 409 LEU 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 804 ASN 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 971 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 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 1563 ASP Chi-restraints excluded: chain A residue 1587 GLU 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 1760 SER 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 1 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 51 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN ** A1414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.165258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.129652 restraints weight = 47480.801| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 4.73 r_work: 0.3483 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10458 Z= 0.125 Angle : 0.664 15.928 14206 Z= 0.332 Chirality : 0.042 0.182 1649 Planarity : 0.004 0.046 1727 Dihedral : 5.848 57.209 1521 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.95 % Favored : 92.81 % Rotamer: Outliers : 2.95 % Allowed : 21.81 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1242 helix: 1.36 (0.19), residues: 765 sheet: -0.43 (0.58), residues: 81 loop : -2.11 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1408 HIS 0.003 0.001 HIS A1393 PHE 0.026 0.001 PHE A1774 TYR 0.014 0.001 TYR A 388 ARG 0.004 0.000 ARG A 862 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 4) link_NAG-ASN : angle 3.27192 ( 12) hydrogen bonds : bond 0.03456 ( 611) hydrogen bonds : angle 3.94476 ( 1725) SS BOND : bond 0.00544 ( 8) SS BOND : angle 1.59738 ( 16) covalent geometry : bond 0.00265 (10446) covalent geometry : angle 0.65609 (14178) ********************** 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 206 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8219 (mmt) cc_final: 0.7801 (mmm) REVERT: A 169 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8369 (p) REVERT: A 424 MET cc_start: 0.8651 (tpt) cc_final: 0.7811 (mtm) REVERT: A 766 MET cc_start: 0.6470 (tpt) cc_final: 0.6221 (tpt) REVERT: A 804 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7269 (t0) REVERT: A 1214 ILE cc_start: 0.8646 (mm) cc_final: 0.8382 (mm) REVERT: A 1219 TRP cc_start: 0.7617 (m-10) cc_final: 0.6939 (m-90) REVERT: A 1266 GLU cc_start: 0.8413 (pp20) cc_final: 0.8124 (pp20) REVERT: A 1267 MET cc_start: 0.8423 (tmm) cc_final: 0.7922 (tmm) REVERT: A 1277 GLN cc_start: 0.8196 (tp40) cc_final: 0.7826 (tp40) REVERT: A 1333 MET cc_start: 0.8375 (mtm) cc_final: 0.7788 (mtp) REVERT: A 1408 TRP cc_start: 0.5929 (t-100) cc_final: 0.5554 (t-100) REVERT: A 1500 MET cc_start: 0.7518 (mtt) cc_final: 0.7172 (mtp) REVERT: A 1608 ASP cc_start: 0.8473 (t70) cc_final: 0.8140 (t70) REVERT: A 1708 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8211 (mt-10) outliers start: 32 outliers final: 20 residues processed: 191 average time/residue: 0.1883 time to fit residues: 54.2110 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 : 1.766 ------------------------------------------------------------------------------- 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 217 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 760 VAL 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 804 ASN Chi-restraints excluded: chain A residue 899 ILE 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 1321 LEU Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1384 ARG 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 60 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.163463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121175 restraints weight = 51808.445| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 4.74 r_work: 0.3446 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10458 Z= 0.146 Angle : 0.679 15.889 14206 Z= 0.339 Chirality : 0.043 0.219 1649 Planarity : 0.004 0.045 1727 Dihedral : 5.824 58.478 1521 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.36 % Favored : 92.48 % Rotamer: Outliers : 3.04 % Allowed : 21.81 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1242 helix: 1.41 (0.19), residues: 765 sheet: -0.33 (0.59), residues: 81 loop : -2.20 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1408 HIS 0.004 0.001 HIS A1393 PHE 0.019 0.001 PHE A1466 TYR 0.021 0.002 TYR A 388 ARG 0.006 0.000 ARG A 862 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 4) link_NAG-ASN : angle 3.30153 ( 12) hydrogen bonds : bond 0.03573 ( 611) hydrogen bonds : angle 3.96971 ( 1725) SS BOND : bond 0.00557 ( 8) SS BOND : angle 1.64973 ( 16) covalent geometry : bond 0.00331 (10446) covalent geometry : angle 0.67019 (14178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6536.06 seconds wall clock time: 115 minutes 3.95 seconds (6903.95 seconds total)