Starting phenix.real_space_refine on Sun May 3 12:06:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j4f_35975/05_2026/8j4f_35975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j4f_35975/05_2026/8j4f_35975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j4f_35975/05_2026/8j4f_35975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j4f_35975/05_2026/8j4f_35975.map" model { file = "/net/cci-nas-00/data/ceres_data/8j4f_35975/05_2026/8j4f_35975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j4f_35975/05_2026/8j4f_35975.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 87 5.16 5 C 8239 2.51 5 N 1870 2.21 5 O 2209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12419 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1273, 10259 Classifications: {'peptide': 1273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1230} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 601 Unusual residues: {'9Z9': 1, 'LPE': 9, 'NAG': 2, 'PCW': 4, 'UK0': 1, 'Y01': 3} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {'LPE': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.17, per 1000 atoms: 0.26 Number of scatterers: 12419 At special positions: 0 Unit cell: (129.552, 130.65, 129.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 P 14 15.00 O 2209 8.00 N 1870 7.00 C 8239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.04 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2001 " - " ASN A 283 " " NAG A2002 " - " ASN A1375 " " NAG B 301 " - " ASN B 110 " " NAG B 302 " - " ASN B 114 " " NAG B 303 " - " ASN B 93 " " NAG C 1 " - " ASN A1366 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN B 135 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 623.0 milliseconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2740 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 5 sheets defined 72.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 16 through 34 Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.918A pdb=" N VAL A 71 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.666A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 125 through 143 removed outlier: 3.529A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.187A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 3.585A pdb=" N ASP A 186 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 206 removed outlier: 3.748A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 219 through 222 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.851A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 267 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.785A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.788A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 removed outlier: 3.762A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 418 Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 742 through 762 removed outlier: 3.667A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 806 through 825 Processing helix chain 'A' and resid 833 through 848 removed outlier: 4.064A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 839 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 840 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.661A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.573A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 973 removed outlier: 3.738A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 3.517A pdb=" N HIS A1191 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1209 through 1212 Processing helix chain 'A' and resid 1215 through 1218 Processing helix chain 'A' and resid 1219 through 1249 Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1278 Processing helix chain 'A' and resid 1283 through 1291 removed outlier: 3.712A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1301 removed outlier: 3.508A pdb=" N ARG A1296 " --> pdb=" O ARG A1293 " (cutoff:3.500A) Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 Proline residue: A1319 - end of helix removed outlier: 3.933A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 4.039A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1467 removed outlier: 3.886A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A1447 " --> pdb=" O PHE A1443 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR A1448 " --> pdb=" O GLY A1444 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A1467 " --> pdb=" O GLN A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1490 removed outlier: 3.530A pdb=" N SER A1490 " --> pdb=" O LYS A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1514 through 1535 removed outlier: 3.659A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A1535 " --> pdb=" O THR A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1569 Processing helix chain 'A' and resid 1570 through 1575 removed outlier: 3.691A pdb=" N PHE A1574 " --> pdb=" O HIS A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 4.222A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1626 Processing helix chain 'A' and resid 1627 through 1666 Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1667 through 1669 No H-bonds generated for 'chain 'A' and resid 1667 through 1669' Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.279A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1708 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1732 through 1767 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.633A pdb=" N GLU B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 153 through 192 removed outlier: 3.552A pdb=" N ALA B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.232A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 38 785 hydrogen bonds defined for protein. 2235 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1851 1.29 - 1.42: 3264 1.42 - 1.55: 7401 1.55 - 1.69: 38 1.69 - 1.82: 142 Bond restraints: 12696 Sorted by residual: bond pdb=" CA SER B 95 " pdb=" CB SER B 95 " ideal model delta sigma weight residual 1.528 1.429 0.099 1.66e-02 3.63e+03 3.59e+01 bond pdb=" C SER B 105 " pdb=" O SER B 105 " ideal model delta sigma weight residual 1.234 1.160 0.075 1.36e-02 5.41e+03 3.02e+01 bond pdb=" C ILE B 106 " pdb=" O ILE B 106 " ideal model delta sigma weight residual 1.233 1.176 0.057 1.08e-02 8.57e+03 2.77e+01 bond pdb=" C ASN B 93 " pdb=" O ASN B 93 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.19e-02 7.06e+03 2.37e+01 bond pdb=" C HIS B 122 " pdb=" O HIS B 122 " ideal model delta sigma weight residual 1.236 1.179 0.057 1.19e-02 7.06e+03 2.28e+01 ... (remaining 12691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 16160 2.07 - 4.14: 808 4.14 - 6.22: 149 6.22 - 8.29: 44 8.29 - 10.36: 7 Bond angle restraints: 17168 Sorted by residual: angle pdb=" CA PHE B 129 " pdb=" C PHE B 129 " pdb=" O PHE B 129 " ideal model delta sigma weight residual 121.58 114.04 7.54 1.16e+00 7.43e-01 4.22e+01 angle pdb=" N ASN B 93 " pdb=" CA ASN B 93 " pdb=" C ASN B 93 " ideal model delta sigma weight residual 108.52 98.53 9.99 1.63e+00 3.76e-01 3.75e+01 angle pdb=" CA TYR B 132 " pdb=" CB TYR B 132 " pdb=" CG TYR B 132 " ideal model delta sigma weight residual 113.90 124.26 -10.36 1.80e+00 3.09e-01 3.31e+01 angle pdb=" CA PHE B 129 " pdb=" CB PHE B 129 " pdb=" CG PHE B 129 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CA PHE B 107 " pdb=" C PHE B 107 " pdb=" O PHE B 107 " ideal model delta sigma weight residual 120.36 114.73 5.63 1.08e+00 8.57e-01 2.71e+01 ... (remaining 17163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.20: 7633 33.20 - 66.40: 372 66.40 - 99.60: 26 99.60 - 132.81: 6 132.81 - 166.01: 1 Dihedral angle restraints: 8038 sinusoidal: 3798 harmonic: 4240 Sorted by residual: dihedral pdb=" C PHE B 107 " pdb=" N PHE B 107 " pdb=" CA PHE B 107 " pdb=" CB PHE B 107 " ideal model delta harmonic sigma weight residual -122.60 -109.73 -12.87 0 2.50e+00 1.60e-01 2.65e+01 dihedral pdb=" C HIS B 122 " pdb=" N HIS B 122 " pdb=" CA HIS B 122 " pdb=" CB HIS B 122 " ideal model delta harmonic sigma weight residual -122.60 -110.25 -12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" N CYS B 121 " pdb=" C CYS B 121 " pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " ideal model delta harmonic sigma weight residual 122.80 111.15 11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 8035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1890 0.146 - 0.291: 68 0.291 - 0.437: 10 0.437 - 0.582: 0 0.582 - 0.728: 1 Chirality restraints: 1969 Sorted by residual: chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 114 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" C1 NAG B 303 " pdb=" ND2 ASN B 93 " pdb=" C2 NAG B 303 " pdb=" O5 NAG B 303 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA GLU B 133 " pdb=" N GLU B 133 " pdb=" C GLU B 133 " pdb=" CB GLU B 133 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1966 not shown) Planarity restraints: 2026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " 0.335 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG B 302 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A2019 " 0.103 2.00e-02 2.50e+03 2.29e-01 5.24e+02 pdb=" C19 PCW A2019 " -0.312 2.00e-02 2.50e+03 pdb=" C20 PCW A2019 " 0.304 2.00e-02 2.50e+03 pdb=" C21 PCW A2019 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.101 2.00e-02 2.50e+03 8.32e-02 8.66e+01 pdb=" C7 NAG C 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.077 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.132 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.019 2.00e-02 2.50e+03 ... (remaining 2023 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1367 2.75 - 3.29: 12252 3.29 - 3.82: 20343 3.82 - 4.36: 24113 4.36 - 4.90: 42021 Nonbonded interactions: 100096 Sorted by model distance: nonbonded pdb=" OH TYR A 392 " pdb=" O LEU A1633 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 318 " pdb=" OG SER A 321 " model vdw 2.228 3.040 nonbonded pdb=" O4 NAG C 1 " pdb=" O6 NAG C 1 " model vdw 2.244 3.040 nonbonded pdb=" O2H LPE A2014 " pdb=" O31 LPE A2014 " model vdw 2.290 3.040 nonbonded pdb=" NZ LYS A1491 " pdb=" O1P PCW A2012 " model vdw 2.327 3.120 ... (remaining 100091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.230 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.008 0.099 12715 Z= 0.490 Angle : 1.033 11.654 17217 Z= 0.626 Chirality : 0.064 0.728 1969 Planarity : 0.010 0.286 2018 Dihedral : 17.706 166.007 5274 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.39 % Allowed : 18.89 % Favored : 79.72 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.22), residues: 1432 helix: 1.95 (0.17), residues: 916 sheet: 1.01 (0.59), residues: 83 loop : -0.28 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 838 TYR 0.042 0.002 TYR B 132 PHE 0.030 0.001 PHE B 129 TRP 0.025 0.002 TRP B 92 HIS 0.009 0.002 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00799 (12696) covalent geometry : angle 1.01911 (17168) SS BOND : bond 0.00513 ( 8) SS BOND : angle 1.48433 ( 16) hydrogen bonds : bond 0.14749 ( 785) hydrogen bonds : angle 5.40178 ( 2235) link_BETA1-4 : bond 0.00804 ( 3) link_BETA1-4 : angle 2.29311 ( 9) link_NAG-ASN : bond 0.01048 ( 8) link_NAG-ASN : angle 4.41874 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.4400 (ptp) cc_final: 0.4160 (ptt) REVERT: A 158 THR cc_start: 0.8332 (m) cc_final: 0.8102 (m) REVERT: A 181 PHE cc_start: 0.7951 (m-80) cc_final: 0.7732 (m-80) REVERT: A 390 SER cc_start: 0.8184 (OUTLIER) cc_final: 0.7911 (m) REVERT: A 742 MET cc_start: 0.6605 (ptt) cc_final: 0.6369 (ptm) REVERT: A 811 PHE cc_start: 0.7560 (t80) cc_final: 0.7197 (t80) REVERT: A 1371 PHE cc_start: 0.7626 (m-10) cc_final: 0.7396 (m-10) REVERT: B 25 ASP cc_start: 0.8218 (m-30) cc_final: 0.7971 (m-30) REVERT: B 120 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8519 (mt-10) outliers start: 18 outliers final: 4 residues processed: 220 average time/residue: 0.5756 time to fit residues: 137.9255 Evaluate side-chains 172 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 144 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 154 ASN A 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.164132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117919 restraints weight = 15617.296| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.24 r_work: 0.3254 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12715 Z= 0.133 Angle : 0.576 9.935 17217 Z= 0.288 Chirality : 0.041 0.310 1969 Planarity : 0.004 0.052 2018 Dihedral : 13.768 168.678 2536 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.95 % Allowed : 19.74 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.22), residues: 1432 helix: 2.20 (0.17), residues: 919 sheet: 0.05 (0.52), residues: 89 loop : 0.05 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1619 TYR 0.017 0.001 TYR A 367 PHE 0.021 0.001 PHE A 176 TRP 0.012 0.001 TRP A 151 HIS 0.006 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00293 (12696) covalent geometry : angle 0.55527 (17168) SS BOND : bond 0.00397 ( 8) SS BOND : angle 1.53551 ( 16) hydrogen bonds : bond 0.04604 ( 785) hydrogen bonds : angle 4.27441 ( 2235) link_BETA1-4 : bond 0.00727 ( 3) link_BETA1-4 : angle 2.82370 ( 9) link_NAG-ASN : bond 0.00903 ( 8) link_NAG-ASN : angle 3.57640 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6104 (mpt) REVERT: A 218 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8202 (t) REVERT: A 742 MET cc_start: 0.5993 (ptt) cc_final: 0.5729 (ptm) REVERT: A 818 LEU cc_start: 0.7696 (mm) cc_final: 0.7488 (mm) REVERT: A 835 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6446 (ttt180) REVERT: A 1269 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8279 (m) REVERT: A 1378 GLN cc_start: 0.7980 (mt0) cc_final: 0.7627 (tm-30) REVERT: A 1590 ILE cc_start: 0.8731 (mt) cc_final: 0.8474 (mp) REVERT: B 25 ASP cc_start: 0.8713 (m-30) cc_final: 0.8474 (m-30) REVERT: B 113 TYR cc_start: 0.7855 (m-80) cc_final: 0.7570 (m-80) REVERT: B 184 LYS cc_start: 0.8356 (mtpp) cc_final: 0.8099 (mmpt) outliers start: 51 outliers final: 15 residues processed: 200 average time/residue: 0.5175 time to fit residues: 113.9803 Evaluate side-chains 178 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 55 optimal weight: 0.0020 chunk 18 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 956 ASN A1459 ASN B 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.164474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118451 restraints weight = 15845.874| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.19 r_work: 0.3276 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12715 Z= 0.112 Angle : 0.508 8.444 17217 Z= 0.256 Chirality : 0.039 0.306 1969 Planarity : 0.003 0.053 2018 Dihedral : 12.662 167.150 2525 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.41 % Allowed : 19.66 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.22), residues: 1432 helix: 2.41 (0.17), residues: 916 sheet: 0.20 (0.52), residues: 91 loop : 0.06 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.015 0.001 TYR A 367 PHE 0.015 0.001 PHE A 176 TRP 0.009 0.001 TRP A 151 HIS 0.005 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00238 (12696) covalent geometry : angle 0.48832 (17168) SS BOND : bond 0.00422 ( 8) SS BOND : angle 1.45267 ( 16) hydrogen bonds : bond 0.03994 ( 785) hydrogen bonds : angle 4.04157 ( 2235) link_BETA1-4 : bond 0.00518 ( 3) link_BETA1-4 : angle 2.72348 ( 9) link_NAG-ASN : bond 0.00667 ( 8) link_NAG-ASN : angle 3.17158 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.4522 (ptp) cc_final: 0.3468 (ptp) REVERT: A 108 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.6019 (mpt) REVERT: A 153 LYS cc_start: 0.7581 (mttt) cc_final: 0.7367 (mmpt) REVERT: A 218 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8324 (t) REVERT: A 791 MET cc_start: 0.8265 (ttp) cc_final: 0.7651 (tmm) REVERT: A 811 PHE cc_start: 0.6993 (t80) cc_final: 0.6734 (t80) REVERT: A 818 LEU cc_start: 0.7796 (mm) cc_final: 0.7588 (mm) REVERT: A 1269 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8349 (m) REVERT: A 1371 PHE cc_start: 0.7798 (m-10) cc_final: 0.7443 (m-10) REVERT: A 1378 GLN cc_start: 0.7854 (mt0) cc_final: 0.7577 (tm-30) REVERT: B 25 ASP cc_start: 0.8699 (m-30) cc_final: 0.8473 (m-30) REVERT: B 113 TYR cc_start: 0.7831 (m-80) cc_final: 0.7524 (m-10) REVERT: B 152 ARG cc_start: 0.8478 (tpt-90) cc_final: 0.8130 (ttt90) REVERT: B 184 LYS cc_start: 0.8401 (mtpp) cc_final: 0.8177 (mmpt) outliers start: 44 outliers final: 13 residues processed: 192 average time/residue: 0.4852 time to fit residues: 102.7858 Evaluate side-chains 171 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1459 ASN B 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.163188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116867 restraints weight = 15651.382| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.98 r_work: 0.3250 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12715 Z= 0.121 Angle : 0.508 8.432 17217 Z= 0.257 Chirality : 0.039 0.304 1969 Planarity : 0.003 0.053 2018 Dihedral : 12.136 167.535 2525 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.33 % Allowed : 19.12 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.22), residues: 1432 helix: 2.37 (0.17), residues: 929 sheet: 0.32 (0.53), residues: 91 loop : -0.18 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 152 TYR 0.026 0.001 TYR A 803 PHE 0.015 0.001 PHE A 216 TRP 0.011 0.001 TRP A1382 HIS 0.006 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00270 (12696) covalent geometry : angle 0.48609 (17168) SS BOND : bond 0.00999 ( 8) SS BOND : angle 2.13995 ( 16) hydrogen bonds : bond 0.03981 ( 785) hydrogen bonds : angle 3.98032 ( 2235) link_BETA1-4 : bond 0.00438 ( 3) link_BETA1-4 : angle 2.73114 ( 9) link_NAG-ASN : bond 0.00634 ( 8) link_NAG-ASN : angle 3.23708 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6078 (mpt) REVERT: A 198 PHE cc_start: 0.6351 (m-10) cc_final: 0.6122 (m-10) REVERT: A 218 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8364 (t) REVERT: A 408 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7109 (mm110) REVERT: A 791 MET cc_start: 0.8199 (ttp) cc_final: 0.7801 (tpp) REVERT: A 796 ILE cc_start: 0.7013 (pt) cc_final: 0.6728 (pp) REVERT: A 803 TYR cc_start: 0.7265 (t80) cc_final: 0.6988 (t80) REVERT: A 811 PHE cc_start: 0.7035 (t80) cc_final: 0.6731 (t80) REVERT: A 818 LEU cc_start: 0.7828 (mm) cc_final: 0.7591 (mm) REVERT: A 844 LYS cc_start: 0.8262 (tmtt) cc_final: 0.7580 (mttm) REVERT: A 1269 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8354 (m) REVERT: A 1371 PHE cc_start: 0.7874 (m-10) cc_final: 0.7564 (m-10) REVERT: A 1458 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8330 (t0) REVERT: A 1630 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7826 (pt) REVERT: B 25 ASP cc_start: 0.8652 (m-30) cc_final: 0.8426 (m-30) REVERT: B 113 TYR cc_start: 0.7845 (m-80) cc_final: 0.7531 (m-10) REVERT: B 152 ARG cc_start: 0.8578 (tpt-90) cc_final: 0.8248 (ttt90) REVERT: B 184 LYS cc_start: 0.8318 (mtpp) cc_final: 0.8091 (mmpt) outliers start: 56 outliers final: 20 residues processed: 204 average time/residue: 0.5084 time to fit residues: 113.7473 Evaluate side-chains 180 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1466 LYS Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A1379 ASN A1459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.164143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120854 restraints weight = 15904.974| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.78 r_work: 0.3264 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12715 Z= 0.108 Angle : 0.505 8.484 17217 Z= 0.254 Chirality : 0.039 0.304 1969 Planarity : 0.003 0.054 2018 Dihedral : 11.751 167.542 2525 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.56 % Allowed : 20.05 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.22), residues: 1432 helix: 2.44 (0.17), residues: 930 sheet: 0.47 (0.55), residues: 84 loop : -0.15 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 994 TYR 0.021 0.001 TYR A 803 PHE 0.024 0.001 PHE A 216 TRP 0.013 0.001 TRP A1408 HIS 0.004 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00235 (12696) covalent geometry : angle 0.48653 (17168) SS BOND : bond 0.00344 ( 8) SS BOND : angle 1.28614 ( 16) hydrogen bonds : bond 0.03777 ( 785) hydrogen bonds : angle 3.88956 ( 2235) link_BETA1-4 : bond 0.00505 ( 3) link_BETA1-4 : angle 2.69941 ( 9) link_NAG-ASN : bond 0.00631 ( 8) link_NAG-ASN : angle 3.12710 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6054 (mpt) REVERT: A 198 PHE cc_start: 0.5907 (m-10) cc_final: 0.5662 (m-80) REVERT: A 216 PHE cc_start: 0.7459 (t80) cc_final: 0.7051 (m-80) REVERT: A 408 GLN cc_start: 0.7402 (mm-40) cc_final: 0.7001 (mm110) REVERT: A 412 ASN cc_start: 0.7763 (m-40) cc_final: 0.7489 (m-40) REVERT: A 773 LYS cc_start: 0.8410 (mtpp) cc_final: 0.7810 (mttp) REVERT: A 791 MET cc_start: 0.8147 (ttp) cc_final: 0.7761 (tpp) REVERT: A 796 ILE cc_start: 0.6974 (pt) cc_final: 0.6734 (pp) REVERT: A 803 TYR cc_start: 0.7220 (t80) cc_final: 0.6905 (t80) REVERT: A 811 PHE cc_start: 0.6998 (t80) cc_final: 0.6617 (t80) REVERT: A 844 LYS cc_start: 0.8165 (tmtt) cc_final: 0.7487 (mttm) REVERT: A 994 ARG cc_start: 0.6262 (tpp-160) cc_final: 0.5474 (mmm160) REVERT: A 1267 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: A 1269 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8271 (m) REVERT: A 1280 TYR cc_start: 0.6418 (m-80) cc_final: 0.6032 (m-10) REVERT: A 1318 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7653 (mt) REVERT: A 1322 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7178 (mmt) REVERT: A 1371 PHE cc_start: 0.7830 (m-10) cc_final: 0.7485 (m-10) REVERT: B 25 ASP cc_start: 0.8663 (m-30) cc_final: 0.8444 (m-30) REVERT: B 113 TYR cc_start: 0.7850 (m-80) cc_final: 0.7543 (m-10) REVERT: B 152 ARG cc_start: 0.8558 (tpt-90) cc_final: 0.8252 (ttt90) REVERT: B 184 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7968 (mmpt) outliers start: 46 outliers final: 23 residues processed: 197 average time/residue: 0.5126 time to fit residues: 111.0395 Evaluate side-chains 188 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1466 LYS Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A1379 ASN A1459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.159805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112411 restraints weight = 15574.403| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.16 r_work: 0.3197 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12715 Z= 0.154 Angle : 0.544 8.358 17217 Z= 0.273 Chirality : 0.041 0.295 1969 Planarity : 0.003 0.054 2018 Dihedral : 11.701 169.087 2525 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.87 % Allowed : 20.05 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.22), residues: 1432 helix: 2.39 (0.17), residues: 925 sheet: 0.51 (0.54), residues: 85 loop : -0.09 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 994 TYR 0.021 0.002 TYR A 803 PHE 0.021 0.002 PHE A 216 TRP 0.009 0.001 TRP A1382 HIS 0.006 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00366 (12696) covalent geometry : angle 0.52266 (17168) SS BOND : bond 0.00629 ( 8) SS BOND : angle 1.94700 ( 16) hydrogen bonds : bond 0.04278 ( 785) hydrogen bonds : angle 3.97001 ( 2235) link_BETA1-4 : bond 0.00598 ( 3) link_BETA1-4 : angle 2.91627 ( 9) link_NAG-ASN : bond 0.00570 ( 8) link_NAG-ASN : angle 3.37385 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.6153 (mpt) REVERT: A 408 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7050 (mm110) REVERT: A 412 ASN cc_start: 0.7807 (m-40) cc_final: 0.7483 (m-40) REVERT: A 791 MET cc_start: 0.8216 (ttp) cc_final: 0.7851 (tpp) REVERT: A 796 ILE cc_start: 0.7005 (pt) cc_final: 0.6757 (pp) REVERT: A 803 TYR cc_start: 0.7261 (t80) cc_final: 0.6971 (t80) REVERT: A 844 LYS cc_start: 0.8235 (tmtt) cc_final: 0.7568 (mttm) REVERT: A 1267 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: A 1269 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8280 (m) REVERT: A 1318 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7748 (mt) REVERT: A 1322 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7429 (mmt) REVERT: A 1630 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7702 (pt) REVERT: B 25 ASP cc_start: 0.8735 (m-30) cc_final: 0.8526 (m-30) REVERT: B 152 ARG cc_start: 0.8630 (tpt-90) cc_final: 0.8353 (ttt90) REVERT: B 184 LYS cc_start: 0.8315 (mtpp) cc_final: 0.7968 (mmpt) outliers start: 50 outliers final: 31 residues processed: 189 average time/residue: 0.5265 time to fit residues: 109.1137 Evaluate side-chains 193 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1466 LYS Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 0.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A1459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.160106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114865 restraints weight = 15448.369| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.64 r_work: 0.3246 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12715 Z= 0.115 Angle : 0.519 8.431 17217 Z= 0.261 Chirality : 0.039 0.301 1969 Planarity : 0.003 0.054 2018 Dihedral : 11.419 169.470 2525 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.10 % Allowed : 21.44 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.22), residues: 1432 helix: 2.56 (0.17), residues: 914 sheet: 0.44 (0.54), residues: 84 loop : 0.12 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A1367 TYR 0.020 0.001 TYR A 803 PHE 0.019 0.001 PHE A1371 TRP 0.013 0.001 TRP A1408 HIS 0.004 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00258 (12696) covalent geometry : angle 0.50012 (17168) SS BOND : bond 0.00401 ( 8) SS BOND : angle 1.47756 ( 16) hydrogen bonds : bond 0.03880 ( 785) hydrogen bonds : angle 3.87641 ( 2235) link_BETA1-4 : bond 0.00499 ( 3) link_BETA1-4 : angle 2.72090 ( 9) link_NAG-ASN : bond 0.00615 ( 8) link_NAG-ASN : angle 3.17213 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6136 (mpt) REVERT: A 408 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7040 (mm110) REVERT: A 412 ASN cc_start: 0.7846 (m-40) cc_final: 0.7513 (m-40) REVERT: A 791 MET cc_start: 0.8208 (ttp) cc_final: 0.7923 (tpp) REVERT: A 796 ILE cc_start: 0.7070 (pt) cc_final: 0.6839 (pp) REVERT: A 803 TYR cc_start: 0.7220 (t80) cc_final: 0.6953 (t80) REVERT: A 844 LYS cc_start: 0.8222 (tmtt) cc_final: 0.7592 (mttm) REVERT: A 1269 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8318 (m) REVERT: A 1318 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7776 (mt) REVERT: A 1322 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7283 (mmt) REVERT: A 1480 LYS cc_start: 0.8041 (mttm) cc_final: 0.7521 (mtmm) REVERT: A 1487 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6574 (mptm) REVERT: A 1630 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7659 (pt) REVERT: B 25 ASP cc_start: 0.8675 (m-30) cc_final: 0.8463 (m-30) REVERT: B 113 TYR cc_start: 0.7916 (m-80) cc_final: 0.7595 (m-10) REVERT: B 152 ARG cc_start: 0.8623 (tpt-90) cc_final: 0.8358 (ttt90) REVERT: B 184 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7992 (mmpt) outliers start: 40 outliers final: 23 residues processed: 187 average time/residue: 0.5104 time to fit residues: 104.9969 Evaluate side-chains 182 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1466 LYS Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 65 optimal weight: 6.9990 chunk 123 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 100 optimal weight: 0.0170 chunk 45 optimal weight: 3.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A1459 ASN B 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.162510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115837 restraints weight = 15512.026| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.70 r_work: 0.3264 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12715 Z= 0.101 Angle : 0.502 8.500 17217 Z= 0.251 Chirality : 0.039 0.303 1969 Planarity : 0.003 0.054 2018 Dihedral : 11.078 169.421 2525 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.10 % Allowed : 21.21 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.22), residues: 1432 helix: 2.61 (0.17), residues: 916 sheet: 0.61 (0.55), residues: 85 loop : 0.15 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1367 TYR 0.021 0.001 TYR A 803 PHE 0.015 0.001 PHE A1371 TRP 0.017 0.001 TRP A 151 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00217 (12696) covalent geometry : angle 0.48366 (17168) SS BOND : bond 0.00305 ( 8) SS BOND : angle 1.25375 ( 16) hydrogen bonds : bond 0.03610 ( 785) hydrogen bonds : angle 3.79885 ( 2235) link_BETA1-4 : bond 0.00563 ( 3) link_BETA1-4 : angle 2.66670 ( 9) link_NAG-ASN : bond 0.00627 ( 8) link_NAG-ASN : angle 3.10516 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6138 (mpt) REVERT: A 408 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7014 (mm110) REVERT: A 412 ASN cc_start: 0.7852 (m-40) cc_final: 0.7505 (m-40) REVERT: A 791 MET cc_start: 0.8185 (ttp) cc_final: 0.7938 (tpp) REVERT: A 803 TYR cc_start: 0.7223 (t80) cc_final: 0.6973 (t80) REVERT: A 844 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7586 (mttm) REVERT: A 910 MET cc_start: 0.9522 (mtt) cc_final: 0.9276 (mmm) REVERT: A 1267 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: A 1269 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8308 (m) REVERT: A 1318 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7770 (mt) REVERT: A 1322 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7280 (mmt) REVERT: A 1371 PHE cc_start: 0.7849 (m-10) cc_final: 0.7559 (m-10) REVERT: A 1457 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 1480 LYS cc_start: 0.8011 (mttm) cc_final: 0.7508 (mtmm) REVERT: A 1487 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6580 (mptm) REVERT: A 1630 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7652 (pt) REVERT: B 25 ASP cc_start: 0.8668 (m-30) cc_final: 0.8450 (m-30) REVERT: B 113 TYR cc_start: 0.7909 (m-80) cc_final: 0.7602 (m-10) REVERT: B 152 ARG cc_start: 0.8642 (tpt-90) cc_final: 0.8372 (ttt90) REVERT: B 184 LYS cc_start: 0.8364 (mtpp) cc_final: 0.7994 (mmpt) outliers start: 40 outliers final: 20 residues processed: 191 average time/residue: 0.4767 time to fit residues: 100.4837 Evaluate side-chains 182 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A1459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.160990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115889 restraints weight = 15417.654| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.63 r_work: 0.3260 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12715 Z= 0.110 Angle : 0.518 8.701 17217 Z= 0.259 Chirality : 0.039 0.303 1969 Planarity : 0.003 0.054 2018 Dihedral : 10.952 169.612 2525 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.55 % Allowed : 21.90 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.23), residues: 1432 helix: 2.61 (0.17), residues: 916 sheet: 0.56 (0.55), residues: 84 loop : 0.16 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1367 TYR 0.021 0.001 TYR A 803 PHE 0.016 0.001 PHE A1371 TRP 0.016 0.001 TRP A 151 HIS 0.004 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00244 (12696) covalent geometry : angle 0.50003 (17168) SS BOND : bond 0.00327 ( 8) SS BOND : angle 1.24665 ( 16) hydrogen bonds : bond 0.03670 ( 785) hydrogen bonds : angle 3.78669 ( 2235) link_BETA1-4 : bond 0.00541 ( 3) link_BETA1-4 : angle 2.66801 ( 9) link_NAG-ASN : bond 0.00612 ( 8) link_NAG-ASN : angle 3.15586 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6156 (mpt) REVERT: A 150 ASP cc_start: 0.8099 (m-30) cc_final: 0.7844 (p0) REVERT: A 168 LEU cc_start: 0.7663 (tm) cc_final: 0.7411 (mm) REVERT: A 408 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7003 (mm110) REVERT: A 412 ASN cc_start: 0.7853 (m-40) cc_final: 0.7499 (m-40) REVERT: A 791 MET cc_start: 0.8163 (ttp) cc_final: 0.7888 (tpp) REVERT: A 803 TYR cc_start: 0.7224 (t80) cc_final: 0.6957 (t80) REVERT: A 844 LYS cc_start: 0.8220 (tmtt) cc_final: 0.7587 (mttm) REVERT: A 910 MET cc_start: 0.9520 (mtt) cc_final: 0.9230 (mmm) REVERT: A 1269 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8314 (m) REVERT: A 1318 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7770 (mt) REVERT: A 1322 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7301 (mmt) REVERT: A 1371 PHE cc_start: 0.7814 (m-10) cc_final: 0.7535 (m-10) REVERT: A 1457 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7862 (pt) REVERT: A 1480 LYS cc_start: 0.8027 (mttm) cc_final: 0.7529 (mtmm) REVERT: A 1487 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6638 (mptt) REVERT: A 1630 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7608 (pt) REVERT: B 25 ASP cc_start: 0.8667 (m-30) cc_final: 0.8449 (m-30) REVERT: B 113 TYR cc_start: 0.7913 (m-80) cc_final: 0.7600 (m-10) REVERT: B 152 ARG cc_start: 0.8645 (tpt-90) cc_final: 0.8395 (ttt90) REVERT: B 172 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8258 (mp) REVERT: B 184 LYS cc_start: 0.8342 (mtpp) cc_final: 0.8098 (mmpt) outliers start: 33 outliers final: 21 residues processed: 176 average time/residue: 0.5071 time to fit residues: 98.5121 Evaluate side-chains 175 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 68 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 86 optimal weight: 0.3980 chunk 12 optimal weight: 0.0770 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A1459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.161405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116386 restraints weight = 15529.868| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.63 r_work: 0.3266 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12715 Z= 0.106 Angle : 0.508 8.882 17217 Z= 0.254 Chirality : 0.039 0.304 1969 Planarity : 0.003 0.054 2018 Dihedral : 10.704 169.699 2525 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.55 % Allowed : 22.14 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.23), residues: 1432 helix: 2.59 (0.17), residues: 917 sheet: 0.67 (0.55), residues: 85 loop : 0.18 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1367 TYR 0.020 0.001 TYR A 803 PHE 0.016 0.001 PHE A1371 TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00231 (12696) covalent geometry : angle 0.48987 (17168) SS BOND : bond 0.00303 ( 8) SS BOND : angle 1.19343 ( 16) hydrogen bonds : bond 0.03600 ( 785) hydrogen bonds : angle 3.78780 ( 2235) link_BETA1-4 : bond 0.00614 ( 3) link_BETA1-4 : angle 2.56637 ( 9) link_NAG-ASN : bond 0.00607 ( 8) link_NAG-ASN : angle 3.15328 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6175 (mpt) REVERT: A 168 LEU cc_start: 0.7692 (tm) cc_final: 0.7339 (mm) REVERT: A 408 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7042 (mm110) REVERT: A 412 ASN cc_start: 0.7886 (m-40) cc_final: 0.7551 (m-40) REVERT: A 816 VAL cc_start: 0.8221 (p) cc_final: 0.7976 (p) REVERT: A 844 LYS cc_start: 0.8231 (tmtt) cc_final: 0.7614 (mttm) REVERT: A 910 MET cc_start: 0.9509 (mtt) cc_final: 0.9270 (mtt) REVERT: A 1269 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8383 (m) REVERT: A 1318 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7803 (mt) REVERT: A 1322 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7319 (mmt) REVERT: A 1371 PHE cc_start: 0.7775 (m-10) cc_final: 0.7481 (m-10) REVERT: A 1457 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7883 (pt) REVERT: A 1480 LYS cc_start: 0.8026 (mttm) cc_final: 0.7535 (mtmm) REVERT: A 1487 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6760 (mptt) REVERT: A 1630 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7631 (pt) REVERT: B 25 ASP cc_start: 0.8693 (m-30) cc_final: 0.8486 (m-30) REVERT: B 113 TYR cc_start: 0.7962 (m-80) cc_final: 0.7657 (m-10) REVERT: B 152 ARG cc_start: 0.8634 (tpt-90) cc_final: 0.8386 (ttt90) REVERT: B 184 LYS cc_start: 0.8299 (mtpp) cc_final: 0.8052 (mmpt) outliers start: 33 outliers final: 22 residues processed: 171 average time/residue: 0.5002 time to fit residues: 94.5754 Evaluate side-chains 173 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1624 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 36 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A1459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.161213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117372 restraints weight = 15735.033| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.84 r_work: 0.3204 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12715 Z= 0.120 Angle : 0.539 8.467 17217 Z= 0.269 Chirality : 0.040 0.303 1969 Planarity : 0.003 0.054 2018 Dihedral : 10.640 170.199 2525 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.71 % Allowed : 22.60 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.23), residues: 1432 helix: 2.54 (0.17), residues: 917 sheet: 0.54 (0.55), residues: 84 loop : 0.15 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1367 TYR 0.018 0.001 TYR A1280 PHE 0.017 0.001 PHE A1371 TRP 0.016 0.001 TRP A 151 HIS 0.004 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00273 (12696) covalent geometry : angle 0.52071 (17168) SS BOND : bond 0.00331 ( 8) SS BOND : angle 1.24815 ( 16) hydrogen bonds : bond 0.03782 ( 785) hydrogen bonds : angle 3.80989 ( 2235) link_BETA1-4 : bond 0.00583 ( 3) link_BETA1-4 : angle 2.62612 ( 9) link_NAG-ASN : bond 0.00586 ( 8) link_NAG-ASN : angle 3.25760 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.22 seconds wall clock time: 81 minutes 6.27 seconds (4866.27 seconds total)