Starting phenix.real_space_refine on Thu Jul 31 17:22:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xm9_33292/07_2025/7xm9_33292_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xm9_33292/07_2025/7xm9_33292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xm9_33292/07_2025/7xm9_33292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xm9_33292/07_2025/7xm9_33292.map" model { file = "/net/cci-nas-00/data/ceres_data/7xm9_33292/07_2025/7xm9_33292_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xm9_33292/07_2025/7xm9_33292_neut.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 963 atoms to isotropic. 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 1 5.49 5 S 97 5.16 5 C 8215 2.51 5 N 1965 2.21 5 O 2212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12490 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9896 Classifications: {'peptide': 1230} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1189} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 977 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {'6OU': 1, 'G2E': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.43, per 1000 atoms: 0.59 Number of scatterers: 12490 At special positions: 0 Unit cell: (126.88, 138.32, 123.76, 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 97 16.00 P 1 15.00 O 2212 8.00 N 1965 7.00 C 8215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=1.65 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.75 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=1.81 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.04 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.03 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=2.61 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.58 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2301 " - " ASN A1375 " " NAG B 501 " - " ASN B 93 " " NAG B 502 " - " ASN B 110 " " NAG B 503 " - " ASN B 114 " " NAG B 504 " - " ASN B 135 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.7 seconds 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 9 sheets defined 65.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.810A 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 144 removed outlier: 4.099A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 3.884A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 204 removed outlier: 3.852A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.751A pdb=" N LEU A 219 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 220 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 removed outlier: 3.944A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 268 removed outlier: 3.557A pdb=" N GLY A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.844A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 417 removed outlier: 5.310A pdb=" N PHE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 Processing helix chain 'A' and resid 742 through 762 removed outlier: 3.671A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 804 Proline residue: A 800 - end of helix Processing helix chain 'A' and resid 806 through 821 Processing helix chain 'A' and resid 834 through 848 removed outlier: 4.258A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 839 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.780A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.328A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 925 Processing helix chain 'A' and resid 928 through 940 removed outlier: 4.114A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 972 removed outlier: 3.548A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 3.857A pdb=" N ASN A1180 " --> pdb=" O LYS A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 4.096A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1255 removed outlier: 4.072A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1284 through 1291 removed outlier: 4.059A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 4.037A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix Processing helix chain 'A' and resid 1366 through 1377 removed outlier: 3.560A pdb=" N ALA A1372 " --> pdb=" O SER A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1408 through 1418 removed outlier: 3.807A pdb=" N ALA A1414 " --> pdb=" O ILE A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1467 removed outlier: 3.817A pdb=" N PHE A1446 " --> pdb=" O ILE A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1487 Processing helix chain 'A' and resid 1488 through 1490 No H-bonds generated for 'chain 'A' and resid 1488 through 1490' Processing helix chain 'A' and resid 1502 through 1514 Processing helix chain 'A' and resid 1514 through 1534 Processing helix chain 'A' and resid 1540 through 1570 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: 3.745A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1626 removed outlier: 3.506A pdb=" N LYS A1625 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1666 removed outlier: 3.931A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 3.879A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1709 Proline residue: A1706 - end of helix removed outlier: 3.895A pdb=" N ASN A1709 " --> pdb=" O ALA A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1752 Processing helix chain 'A' and resid 1754 through 1769 removed outlier: 3.532A pdb=" N GLU A1769 " --> pdb=" O VAL A1765 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.595A pdb=" N PHE B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 87' Processing helix chain 'B' and resid 153 through 191 removed outlier: 3.584A pdb=" N THR B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 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 1349 through 1352 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.487A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.487A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA7, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.114A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.302A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 46 through 48 787 hydrogen bonds defined for protein. 2232 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: 4.66 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.34: 3765 1.34 - 1.51: 3834 1.51 - 1.67: 5032 1.67 - 1.84: 154 1.84 - 2.01: 2 Bond restraints: 12787 Sorted by residual: bond pdb=" C12 G2E A2302 " pdb=" O01 G2E A2302 " ideal model delta sigma weight residual 1.351 1.574 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C12 G2E A2302 " pdb=" C18 G2E A2302 " ideal model delta sigma weight residual 1.394 1.602 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C08 G2E A2302 " pdb=" C14 G2E A2302 " ideal model delta sigma weight residual 1.394 1.590 -0.196 2.00e-02 2.50e+03 9.63e+01 bond pdb=" C17 G2E A2302 " pdb=" C23 G2E A2302 " ideal model delta sigma weight residual 1.394 1.555 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" C07 G2E A2302 " pdb=" C15 G2E A2302 " ideal model delta sigma weight residual 1.378 1.534 -0.156 2.00e-02 2.50e+03 6.07e+01 ... (remaining 12782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 17191 3.98 - 7.95: 109 7.95 - 11.93: 10 11.93 - 15.91: 6 15.91 - 19.89: 1 Bond angle restraints: 17317 Sorted by residual: angle pdb=" N TYR A 801 " pdb=" CA TYR A 801 " pdb=" C TYR A 801 " ideal model delta sigma weight residual 111.40 125.24 -13.84 1.22e+00 6.72e-01 1.29e+02 angle pdb=" N MET A 379 " pdb=" CA MET A 379 " pdb=" C MET A 379 " ideal model delta sigma weight residual 111.82 102.70 9.12 1.16e+00 7.43e-01 6.19e+01 angle pdb=" C ASN C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 119.66 114.10 5.56 7.20e-01 1.93e+00 5.97e+01 angle pdb=" N GLU A 802 " pdb=" CA GLU A 802 " pdb=" C GLU A 802 " ideal model delta sigma weight residual 112.89 103.88 9.01 1.24e+00 6.50e-01 5.28e+01 angle pdb=" C09 G2E A2302 " pdb=" C06 G2E A2302 " pdb=" C10 G2E A2302 " ideal model delta sigma weight residual 112.09 92.20 19.89 3.00e+00 1.11e-01 4.39e+01 ... (remaining 17312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 7049 24.08 - 48.17: 549 48.17 - 72.25: 87 72.25 - 96.33: 19 96.33 - 120.41: 4 Dihedral angle restraints: 7708 sinusoidal: 3243 harmonic: 4465 Sorted by residual: dihedral pdb=" CA GLY A 322 " pdb=" C GLY A 322 " pdb=" N GLN A 323 " pdb=" CA GLN A 323 " ideal model delta harmonic sigma weight residual -180.00 -59.59 -120.41 0 5.00e+00 4.00e-02 5.80e+02 dihedral pdb=" CB CYS A1350 " pdb=" SG CYS A1350 " pdb=" SG CYS A1370 " pdb=" CB CYS A1370 " ideal model delta sinusoidal sigma weight residual -86.00 -161.56 75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual -86.00 -161.51 75.51 1 1.00e+01 1.00e-02 7.20e+01 ... (remaining 7705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1879 0.096 - 0.192: 100 0.192 - 0.288: 13 0.288 - 0.384: 3 0.384 - 0.479: 2 Chirality restraints: 1997 Sorted by residual: chirality pdb=" CA PHE A1679 " pdb=" N PHE A1679 " pdb=" C PHE A1679 " pdb=" CB PHE A1679 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA CYS A 897 " pdb=" N CYS A 897 " pdb=" C CYS A 897 " pdb=" CB CYS A 897 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA ASP A 320 " pdb=" N ASP A 320 " pdb=" C ASP A 320 " pdb=" CB ASP A 320 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 1994 not shown) Planarity restraints: 2123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 104 " 0.061 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO C 105 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 105 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 105 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 378 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR A 378 " 0.056 2.00e-02 2.50e+03 pdb=" O TYR A 378 " -0.021 2.00e-02 2.50e+03 pdb=" N MET A 379 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 132 " -0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO C 133 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 133 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 133 " -0.043 5.00e-02 4.00e+02 ... (remaining 2120 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 83 2.53 - 3.12: 9921 3.12 - 3.71: 19312 3.71 - 4.31: 27088 4.31 - 4.90: 45070 Nonbonded interactions: 101474 Sorted by model distance: nonbonded pdb=" OD1 ASP A 361 " pdb=" O GLY A 926 " model vdw 1.933 3.040 nonbonded pdb=" CD2 TYR C 128 " pdb=" NH2 ARG C 137 " model vdw 2.087 3.420 nonbonded pdb=" O GLN C 62 " pdb=" CD PRO C 132 " model vdw 2.107 3.440 nonbonded pdb=" CE2 PHE C 101 " pdb=" O GLY C 103 " model vdw 2.108 3.340 nonbonded pdb=" O GLY A1444 " pdb=" OG1 THR A1448 " model vdw 2.163 3.040 ... (remaining 101469 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 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.540 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 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 : 0.013 0.714 12807 Z= 0.645 Angle : 1.026 50.459 17366 Z= 0.552 Chirality : 0.053 0.479 1997 Planarity : 0.005 0.093 2116 Dihedral : 17.017 120.415 4791 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.71 % Favored : 95.03 % Rotamer: Outliers : 3.45 % Allowed : 15.99 % Favored : 80.56 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.20), residues: 1509 helix: -0.81 (0.15), residues: 850 sheet: -0.98 (0.43), residues: 136 loop : -1.91 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.004 0.001 HIS A 273 PHE 0.020 0.002 PHE A 963 TYR 0.018 0.001 TYR C 125 ARG 0.003 0.000 ARG A 835 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 7) link_NAG-ASN : angle 2.06218 ( 21) link_BETA1-4 : bond 0.00531 ( 2) link_BETA1-4 : angle 3.77264 ( 6) hydrogen bonds : bond 0.12365 ( 777) hydrogen bonds : angle 5.87493 ( 2232) SS BOND : bond 0.35026 ( 11) SS BOND : angle 15.69353 ( 22) covalent geometry : bond 0.00745 (12787) covalent geometry : angle 0.85648 (17317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 325 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.8349 (m-80) cc_final: 0.8063 (m-80) REVERT: A 130 MET cc_start: 0.6792 (mmt) cc_final: 0.6496 (mmt) REVERT: A 151 TRP cc_start: 0.7453 (p-90) cc_final: 0.6983 (p90) REVERT: A 156 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6662 (pt0) REVERT: A 184 LEU cc_start: 0.8512 (mt) cc_final: 0.8273 (mt) REVERT: A 217 ARG cc_start: 0.7913 (ptp-110) cc_final: 0.7264 (mtm-85) REVERT: A 249 MET cc_start: 0.6202 (mmm) cc_final: 0.5884 (mmm) REVERT: A 289 ILE cc_start: 0.9007 (mm) cc_final: 0.8554 (mm) REVERT: A 364 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: A 398 LEU cc_start: 0.8253 (mp) cc_final: 0.8037 (mp) REVERT: A 761 MET cc_start: 0.8138 (ttm) cc_final: 0.7935 (mtp) REVERT: A 770 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 773 LYS cc_start: 0.8789 (tptp) cc_final: 0.8262 (ttmt) REVERT: A 901 ASP cc_start: 0.7540 (m-30) cc_final: 0.7273 (t0) REVERT: A 948 TYR cc_start: 0.7990 (m-80) cc_final: 0.7543 (m-80) REVERT: A 957 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8371 (tp) REVERT: A 961 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8513 (m-40) REVERT: A 1188 ILE cc_start: 0.8738 (mm) cc_final: 0.8472 (mm) REVERT: A 1196 SER cc_start: 0.8377 (t) cc_final: 0.8035 (m) REVERT: A 1251 LYS cc_start: 0.7852 (tttt) cc_final: 0.7557 (pttm) REVERT: A 1252 THR cc_start: 0.8961 (m) cc_final: 0.8694 (p) REVERT: A 1331 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 1410 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8618 (pt) REVERT: A 1449 LEU cc_start: 0.7575 (tp) cc_final: 0.6808 (mp) REVERT: A 1452 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.6211 (m-80) REVERT: A 1542 HIS cc_start: 0.7715 (t70) cc_final: 0.7486 (t-170) REVERT: A 1550 ILE cc_start: 0.8275 (mm) cc_final: 0.8017 (mt) REVERT: A 1613 ARG cc_start: 0.8424 (mtp180) cc_final: 0.8170 (mtp85) REVERT: B 60 ARG cc_start: 0.8075 (ptt180) cc_final: 0.7666 (ptt-90) REVERT: B 99 LYS cc_start: 0.8220 (tptm) cc_final: 0.7915 (tptm) REVERT: B 152 ARG cc_start: 0.7469 (ttm-80) cc_final: 0.7009 (mtp85) REVERT: B 178 MET cc_start: 0.8101 (mtt) cc_final: 0.7343 (tmm) REVERT: B 182 TYR cc_start: 0.8468 (t80) cc_final: 0.8182 (t80) outliers start: 47 outliers final: 22 residues processed: 361 average time/residue: 0.2418 time to fit residues: 126.0315 Evaluate side-chains 297 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1191 HIS Chi-restraints excluded: chain A residue 1236 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain A residue 1675 ILE Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 34 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 88 optimal weight: 0.0010 chunk 138 optimal weight: 7.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 139 ASN A 146 ASN A 278 ASN A 395 ASN A 412 ASN A 757 ASN A 765 HIS A 809 ASN A 909 HIS A 911 ASN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 ASN A1424 GLN A1459 ASN A1502 ASN A1579 ASN A1709 ASN A1753 ASN A1762 ASN B 50 ASN B 102 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS C 118 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.197099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141050 restraints weight = 14773.990| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.60 r_work: 0.3337 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12807 Z= 0.147 Angle : 0.665 9.994 17366 Z= 0.334 Chirality : 0.043 0.261 1997 Planarity : 0.005 0.051 2116 Dihedral : 10.898 100.310 1953 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.96 % Allowed : 19.44 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1509 helix: 0.67 (0.17), residues: 852 sheet: -1.28 (0.41), residues: 141 loop : -1.46 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 67 HIS 0.007 0.001 HIS A 273 PHE 0.016 0.001 PHE B 54 TYR 0.014 0.001 TYR A1739 ARG 0.007 0.001 ARG C 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 7) link_NAG-ASN : angle 1.70280 ( 21) link_BETA1-4 : bond 0.00299 ( 2) link_BETA1-4 : angle 4.01401 ( 6) hydrogen bonds : bond 0.04062 ( 777) hydrogen bonds : angle 4.84409 ( 2232) SS BOND : bond 0.00774 ( 11) SS BOND : angle 1.89211 ( 22) covalent geometry : bond 0.00316 (12787) covalent geometry : angle 0.65536 (17317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.8410 (m-80) cc_final: 0.7983 (m-80) REVERT: A 145 MET cc_start: 0.8531 (mmm) cc_final: 0.8321 (mmm) REVERT: A 151 TRP cc_start: 0.7549 (p-90) cc_final: 0.7117 (p90) REVERT: A 156 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7225 (pt0) REVERT: A 216 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8305 (t80) REVERT: A 217 ARG cc_start: 0.8120 (ptp-110) cc_final: 0.7469 (mtm-85) REVERT: A 240 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: A 289 ILE cc_start: 0.9228 (mm) cc_final: 0.8940 (mm) REVERT: A 364 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: A 398 LEU cc_start: 0.8573 (mp) cc_final: 0.8371 (mp) REVERT: A 408 GLN cc_start: 0.7807 (tp40) cc_final: 0.7527 (tp40) REVERT: A 773 LYS cc_start: 0.8729 (tptp) cc_final: 0.8420 (ttmt) REVERT: A 948 TYR cc_start: 0.8224 (m-80) cc_final: 0.7874 (m-80) REVERT: A 1188 ILE cc_start: 0.8958 (mm) cc_final: 0.8701 (mm) REVERT: A 1196 SER cc_start: 0.8530 (t) cc_final: 0.8214 (m) REVERT: A 1251 LYS cc_start: 0.8240 (tttt) cc_final: 0.7856 (pttm) REVERT: A 1331 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7431 (t80) REVERT: A 1481 TYR cc_start: 0.7601 (m-80) cc_final: 0.7382 (m-10) REVERT: A 1515 GLN cc_start: 0.7895 (pt0) cc_final: 0.7662 (pt0) REVERT: A 1524 LEU cc_start: 0.8449 (mm) cc_final: 0.8182 (mm) REVERT: A 1609 PHE cc_start: 0.8277 (t80) cc_final: 0.7899 (t80) REVERT: B 62 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7969 (ttpt) REVERT: B 152 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7387 (mtp85) REVERT: B 178 MET cc_start: 0.8028 (mtt) cc_final: 0.7431 (tmm) REVERT: C 85 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.4838 (mmt) outliers start: 54 outliers final: 29 residues processed: 315 average time/residue: 0.2336 time to fit residues: 108.1696 Evaluate side-chains 287 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1386 LYS Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 85 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 150 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.0270 chunk 1 optimal weight: 20.0000 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A1505 GLN A1528 ASN A1753 ASN B 102 GLN B 115 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.189499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119376 restraints weight = 14837.620| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.12 r_work: 0.3185 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 12807 Z= 0.188 Angle : 0.648 9.933 17366 Z= 0.327 Chirality : 0.043 0.291 1997 Planarity : 0.004 0.046 2116 Dihedral : 9.785 96.860 1918 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.40 % Allowed : 20.91 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1509 helix: 1.04 (0.17), residues: 850 sheet: -1.15 (0.40), residues: 139 loop : -1.26 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1700 HIS 0.008 0.001 HIS A1542 PHE 0.018 0.002 PHE A 159 TYR 0.017 0.002 TYR A1739 ARG 0.003 0.000 ARG B 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 7) link_NAG-ASN : angle 1.75933 ( 21) link_BETA1-4 : bond 0.00778 ( 2) link_BETA1-4 : angle 4.05095 ( 6) hydrogen bonds : bond 0.04040 ( 777) hydrogen bonds : angle 4.74413 ( 2232) SS BOND : bond 0.00666 ( 11) SS BOND : angle 1.64463 ( 22) covalent geometry : bond 0.00438 (12787) covalent geometry : angle 0.63924 (17317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 260 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.8077 (m-80) cc_final: 0.7657 (m-80) REVERT: A 133 MET cc_start: 0.7296 (mmm) cc_final: 0.7095 (tpp) REVERT: A 151 TRP cc_start: 0.7454 (p-90) cc_final: 0.6970 (p90) REVERT: A 156 GLU cc_start: 0.7770 (mm-30) cc_final: 0.6800 (pt0) REVERT: A 214 ARG cc_start: 0.7891 (ttt90) cc_final: 0.7660 (ttt90) REVERT: A 216 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8217 (t80) REVERT: A 217 ARG cc_start: 0.8018 (ptp-110) cc_final: 0.7379 (mtm-85) REVERT: A 240 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6646 (mp10) REVERT: A 288 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 364 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: A 398 LEU cc_start: 0.8390 (mp) cc_final: 0.8190 (mp) REVERT: A 408 GLN cc_start: 0.7178 (tp40) cc_final: 0.6026 (pt0) REVERT: A 773 LYS cc_start: 0.8416 (tptp) cc_final: 0.7985 (ttmt) REVERT: A 798 MET cc_start: 0.5524 (mmp) cc_final: 0.5253 (mmp) REVERT: A 948 TYR cc_start: 0.8401 (m-80) cc_final: 0.7715 (m-80) REVERT: A 1188 ILE cc_start: 0.8683 (mm) cc_final: 0.8383 (mm) REVERT: A 1196 SER cc_start: 0.8439 (t) cc_final: 0.8136 (m) REVERT: A 1251 LYS cc_start: 0.7648 (tttt) cc_final: 0.7069 (pttm) REVERT: A 1262 ASP cc_start: 0.8091 (m-30) cc_final: 0.7707 (m-30) REVERT: A 1305 GLU cc_start: 0.7014 (pm20) cc_final: 0.6593 (pm20) REVERT: A 1331 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7552 (t80) REVERT: A 1609 PHE cc_start: 0.8238 (t80) cc_final: 0.7720 (t80) REVERT: A 1613 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7432 (mtp180) REVERT: B 62 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7920 (ttpt) REVERT: B 120 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7657 (mm-30) REVERT: B 152 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7017 (ttp80) REVERT: B 178 MET cc_start: 0.8201 (mtt) cc_final: 0.7296 (tmm) REVERT: C 85 MET cc_start: 0.5558 (OUTLIER) cc_final: 0.5054 (mmt) outliers start: 60 outliers final: 34 residues processed: 302 average time/residue: 0.2164 time to fit residues: 98.0206 Evaluate side-chains 290 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1191 HIS Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 85 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 265 GLN A 278 ASN A 809 ASN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN A1753 ASN C 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.188968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118980 restraints weight = 14674.191| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.11 r_work: 0.3162 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 12807 Z= 0.193 Angle : 0.638 9.877 17366 Z= 0.320 Chirality : 0.043 0.291 1997 Planarity : 0.004 0.040 2116 Dihedral : 9.325 94.944 1915 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.92 % Allowed : 20.91 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1509 helix: 1.17 (0.17), residues: 859 sheet: -0.97 (0.41), residues: 139 loop : -1.19 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1408 HIS 0.005 0.001 HIS A1542 PHE 0.017 0.002 PHE A1740 TYR 0.019 0.002 TYR A1548 ARG 0.002 0.000 ARG A1631 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 7) link_NAG-ASN : angle 1.77145 ( 21) link_BETA1-4 : bond 0.01045 ( 2) link_BETA1-4 : angle 4.02581 ( 6) hydrogen bonds : bond 0.03966 ( 777) hydrogen bonds : angle 4.69321 ( 2232) SS BOND : bond 0.00583 ( 11) SS BOND : angle 1.38956 ( 22) covalent geometry : bond 0.00451 (12787) covalent geometry : angle 0.62939 (17317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7989 (m-80) cc_final: 0.7637 (m-80) REVERT: A 133 MET cc_start: 0.7406 (mmm) cc_final: 0.7121 (tpp) REVERT: A 151 TRP cc_start: 0.7538 (p-90) cc_final: 0.7069 (p90) REVERT: A 156 GLU cc_start: 0.7766 (mm-30) cc_final: 0.6797 (pt0) REVERT: A 214 ARG cc_start: 0.7856 (ttt90) cc_final: 0.7631 (ttt90) REVERT: A 216 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8243 (t80) REVERT: A 217 ARG cc_start: 0.7985 (ptp-110) cc_final: 0.7314 (mtm-85) REVERT: A 240 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6613 (mp10) REVERT: A 364 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: A 379 MET cc_start: 0.8421 (tmm) cc_final: 0.8116 (tmm) REVERT: A 406 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7060 (tm-30) REVERT: A 407 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6965 (mm-30) REVERT: A 408 GLN cc_start: 0.7090 (tp40) cc_final: 0.6028 (pt0) REVERT: A 773 LYS cc_start: 0.8560 (tptp) cc_final: 0.7993 (ttmt) REVERT: A 1188 ILE cc_start: 0.8629 (mm) cc_final: 0.8336 (mm) REVERT: A 1196 SER cc_start: 0.8493 (t) cc_final: 0.8208 (m) REVERT: A 1251 LYS cc_start: 0.7917 (tttt) cc_final: 0.7332 (pttm) REVERT: A 1331 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7660 (t80) REVERT: A 1524 LEU cc_start: 0.8370 (mm) cc_final: 0.8132 (mm) REVERT: A 1579 ASN cc_start: 0.8657 (m110) cc_final: 0.8285 (m-40) REVERT: A 1609 PHE cc_start: 0.8216 (t80) cc_final: 0.7944 (t80) REVERT: A 1613 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7447 (mtp180) REVERT: B 62 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7908 (ttpt) REVERT: B 120 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7598 (mm-30) REVERT: B 152 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.6964 (ttp80) REVERT: B 178 MET cc_start: 0.8067 (mtt) cc_final: 0.7133 (tmm) REVERT: B 182 TYR cc_start: 0.8542 (t80) cc_final: 0.7991 (t80) REVERT: C 85 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5223 (mmt) outliers start: 67 outliers final: 42 residues processed: 291 average time/residue: 0.2180 time to fit residues: 95.6393 Evaluate side-chains 285 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1191 HIS Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 85 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 136 optimal weight: 0.0040 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 360 GLN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN A1753 ASN C 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.190139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120974 restraints weight = 14668.946| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.12 r_work: 0.3192 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12807 Z= 0.140 Angle : 0.601 9.748 17366 Z= 0.301 Chirality : 0.042 0.268 1997 Planarity : 0.004 0.038 2116 Dihedral : 9.169 94.823 1915 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.26 % Allowed : 22.08 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1509 helix: 1.37 (0.17), residues: 862 sheet: -0.83 (0.42), residues: 139 loop : -1.13 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1700 HIS 0.005 0.001 HIS A 14 PHE 0.017 0.001 PHE A 12 TYR 0.017 0.001 TYR A1739 ARG 0.002 0.000 ARG A1631 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 7) link_NAG-ASN : angle 1.65061 ( 21) link_BETA1-4 : bond 0.00751 ( 2) link_BETA1-4 : angle 3.95871 ( 6) hydrogen bonds : bond 0.03821 ( 777) hydrogen bonds : angle 4.59843 ( 2232) SS BOND : bond 0.00483 ( 11) SS BOND : angle 1.13898 ( 22) covalent geometry : bond 0.00313 (12787) covalent geometry : angle 0.59329 (17317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7954 (m-80) cc_final: 0.7641 (m-80) REVERT: A 151 TRP cc_start: 0.7585 (p-90) cc_final: 0.7131 (p90) REVERT: A 156 GLU cc_start: 0.7796 (mm-30) cc_final: 0.6829 (pt0) REVERT: A 214 ARG cc_start: 0.7863 (ttt90) cc_final: 0.7639 (ttt90) REVERT: A 217 ARG cc_start: 0.7989 (ptp-110) cc_final: 0.7292 (mtm-85) REVERT: A 240 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6573 (mp10) REVERT: A 288 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8825 (p) REVERT: A 379 MET cc_start: 0.8382 (tmm) cc_final: 0.8062 (tmm) REVERT: A 406 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7099 (tm-30) REVERT: A 407 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7025 (mm-30) REVERT: A 408 GLN cc_start: 0.7227 (tp40) cc_final: 0.6174 (pt0) REVERT: A 773 LYS cc_start: 0.8598 (tptp) cc_final: 0.8027 (ttmt) REVERT: A 948 TYR cc_start: 0.8403 (m-80) cc_final: 0.7750 (m-80) REVERT: A 964 LEU cc_start: 0.8649 (mm) cc_final: 0.8448 (mp) REVERT: A 1188 ILE cc_start: 0.8636 (mm) cc_final: 0.8337 (mm) REVERT: A 1196 SER cc_start: 0.8524 (t) cc_final: 0.8208 (m) REVERT: A 1251 LYS cc_start: 0.7905 (tttt) cc_final: 0.7347 (pttm) REVERT: A 1305 GLU cc_start: 0.7171 (pm20) cc_final: 0.5975 (tt0) REVERT: A 1331 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7731 (t80) REVERT: A 1579 ASN cc_start: 0.8666 (m110) cc_final: 0.8312 (m-40) REVERT: A 1609 PHE cc_start: 0.8197 (t80) cc_final: 0.7937 (t80) REVERT: A 1613 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7437 (mtp180) REVERT: B 62 LYS cc_start: 0.8365 (ttmt) cc_final: 0.7926 (ttpt) REVERT: B 119 TYR cc_start: 0.8853 (m-80) cc_final: 0.8486 (m-80) REVERT: B 120 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 152 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.6950 (ttp80) REVERT: B 154 MET cc_start: 0.6902 (ttp) cc_final: 0.6687 (tmm) REVERT: B 178 MET cc_start: 0.8114 (mtt) cc_final: 0.7169 (tmm) REVERT: B 182 TYR cc_start: 0.8547 (t80) cc_final: 0.8021 (t80) REVERT: C 85 MET cc_start: 0.5664 (mmm) cc_final: 0.5271 (mmt) outliers start: 58 outliers final: 46 residues processed: 283 average time/residue: 0.2160 time to fit residues: 92.9816 Evaluate side-chains 288 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1191 HIS Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1455 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 144 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN B 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.189520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119261 restraints weight = 14852.765| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.16 r_work: 0.3190 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12807 Z= 0.171 Angle : 0.619 9.907 17366 Z= 0.308 Chirality : 0.042 0.272 1997 Planarity : 0.004 0.038 2116 Dihedral : 8.893 93.795 1912 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.77 % Allowed : 22.38 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1509 helix: 1.45 (0.17), residues: 856 sheet: -0.77 (0.42), residues: 139 loop : -1.02 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1700 HIS 0.013 0.001 HIS A 14 PHE 0.028 0.001 PHE A 165 TYR 0.018 0.001 TYR A1548 ARG 0.002 0.000 ARG A1631 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 7) link_NAG-ASN : angle 1.67507 ( 21) link_BETA1-4 : bond 0.00786 ( 2) link_BETA1-4 : angle 4.00483 ( 6) hydrogen bonds : bond 0.03848 ( 777) hydrogen bonds : angle 4.59502 ( 2232) SS BOND : bond 0.00521 ( 11) SS BOND : angle 1.18479 ( 22) covalent geometry : bond 0.00395 (12787) covalent geometry : angle 0.61144 (17317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 241 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7990 (m-80) cc_final: 0.7674 (m-80) REVERT: A 151 TRP cc_start: 0.7596 (p-90) cc_final: 0.7121 (p90) REVERT: A 156 GLU cc_start: 0.7798 (mm-30) cc_final: 0.6694 (pt0) REVERT: A 240 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6542 (mp10) REVERT: A 403 MET cc_start: 0.7885 (tpp) cc_final: 0.7557 (tpp) REVERT: A 406 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7144 (tm-30) REVERT: A 407 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7076 (mm-30) REVERT: A 408 GLN cc_start: 0.7266 (tp40) cc_final: 0.6219 (pt0) REVERT: A 773 LYS cc_start: 0.8607 (tptp) cc_final: 0.8045 (ttmt) REVERT: A 964 LEU cc_start: 0.8669 (mm) cc_final: 0.8460 (mp) REVERT: A 1188 ILE cc_start: 0.8654 (mm) cc_final: 0.8359 (mm) REVERT: A 1196 SER cc_start: 0.8586 (t) cc_final: 0.8230 (m) REVERT: A 1251 LYS cc_start: 0.7954 (tttt) cc_final: 0.7353 (pttm) REVERT: A 1305 GLU cc_start: 0.7148 (pm20) cc_final: 0.5915 (tt0) REVERT: A 1331 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7695 (t80) REVERT: A 1452 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.5933 (m-10) REVERT: A 1524 LEU cc_start: 0.8406 (mm) cc_final: 0.8173 (mm) REVERT: A 1529 MET cc_start: 0.7933 (ttt) cc_final: 0.7690 (ttt) REVERT: A 1579 ASN cc_start: 0.8741 (m110) cc_final: 0.8405 (m-40) REVERT: A 1609 PHE cc_start: 0.8228 (t80) cc_final: 0.7961 (t80) REVERT: B 62 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7968 (ttpt) REVERT: B 119 TYR cc_start: 0.8871 (m-80) cc_final: 0.8468 (m-80) REVERT: B 120 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 152 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7074 (ttp80) REVERT: B 154 MET cc_start: 0.7044 (ttp) cc_final: 0.6782 (tmm) REVERT: B 178 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7147 (tmm) REVERT: B 182 TYR cc_start: 0.8596 (t80) cc_final: 0.8098 (t80) REVERT: C 85 MET cc_start: 0.5737 (mmm) cc_final: 0.5376 (mmt) outliers start: 65 outliers final: 50 residues processed: 283 average time/residue: 0.2007 time to fit residues: 87.5606 Evaluate side-chains 281 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1455 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1677 ASP Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.0030 chunk 46 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN B 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.190458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120715 restraints weight = 14741.750| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.15 r_work: 0.3189 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12807 Z= 0.145 Angle : 0.601 10.009 17366 Z= 0.300 Chirality : 0.042 0.266 1997 Planarity : 0.004 0.038 2116 Dihedral : 8.599 92.346 1912 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.62 % Allowed : 23.18 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1509 helix: 1.60 (0.17), residues: 856 sheet: -0.70 (0.42), residues: 136 loop : -0.97 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1700 HIS 0.006 0.001 HIS A1542 PHE 0.014 0.001 PHE A 100 TYR 0.016 0.001 TYR A 367 ARG 0.003 0.000 ARG A1616 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 7) link_NAG-ASN : angle 1.54766 ( 21) link_BETA1-4 : bond 0.00650 ( 2) link_BETA1-4 : angle 3.97294 ( 6) hydrogen bonds : bond 0.03747 ( 777) hydrogen bonds : angle 4.55623 ( 2232) SS BOND : bond 0.00439 ( 11) SS BOND : angle 1.08336 ( 22) covalent geometry : bond 0.00329 (12787) covalent geometry : angle 0.59377 (17317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7937 (m-80) cc_final: 0.7631 (m-80) REVERT: A 151 TRP cc_start: 0.7474 (p-90) cc_final: 0.7003 (p90) REVERT: A 156 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6678 (pt0) REVERT: A 170 LYS cc_start: 0.7587 (ttmt) cc_final: 0.7361 (mtpt) REVERT: A 240 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6485 (mp10) REVERT: A 406 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 407 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7180 (mm-30) REVERT: A 408 GLN cc_start: 0.7287 (tp40) cc_final: 0.6269 (pt0) REVERT: A 763 MET cc_start: 0.9031 (ttp) cc_final: 0.8828 (ttp) REVERT: A 773 LYS cc_start: 0.8616 (tptp) cc_final: 0.8053 (ttmt) REVERT: A 1188 ILE cc_start: 0.8611 (mm) cc_final: 0.8307 (mm) REVERT: A 1196 SER cc_start: 0.8576 (t) cc_final: 0.8220 (m) REVERT: A 1251 LYS cc_start: 0.7894 (tttt) cc_final: 0.7283 (pttm) REVERT: A 1305 GLU cc_start: 0.7128 (pm20) cc_final: 0.5900 (tt0) REVERT: A 1331 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7760 (t80) REVERT: A 1452 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.5939 (m-10) REVERT: A 1543 MET cc_start: 0.8717 (ttt) cc_final: 0.8480 (ttt) REVERT: A 1579 ASN cc_start: 0.8744 (m110) cc_final: 0.8401 (m-40) REVERT: A 1609 PHE cc_start: 0.8185 (t80) cc_final: 0.7909 (t80) REVERT: A 1753 ASN cc_start: 0.9018 (m-40) cc_final: 0.8756 (m110) REVERT: B 62 LYS cc_start: 0.8405 (ttmt) cc_final: 0.7957 (ttpt) REVERT: B 152 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7086 (ttp80) REVERT: B 154 MET cc_start: 0.7108 (ttp) cc_final: 0.6792 (tmm) REVERT: B 178 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7125 (tmm) REVERT: B 182 TYR cc_start: 0.8637 (t80) cc_final: 0.8181 (t80) REVERT: C 85 MET cc_start: 0.5735 (mmm) cc_final: 0.5377 (mmt) outliers start: 63 outliers final: 49 residues processed: 288 average time/residue: 0.2064 time to fit residues: 91.9663 Evaluate side-chains 286 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 233 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1677 ASP Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN B 102 GLN C 143 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.189623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119687 restraints weight = 14837.601| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.17 r_work: 0.3129 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 12807 Z= 0.171 Angle : 0.623 10.387 17366 Z= 0.310 Chirality : 0.043 0.270 1997 Planarity : 0.004 0.038 2116 Dihedral : 8.470 89.955 1912 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.84 % Favored : 95.10 % Rotamer: Outliers : 4.84 % Allowed : 23.26 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1509 helix: 1.59 (0.17), residues: 852 sheet: -0.68 (0.40), residues: 142 loop : -0.96 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1700 HIS 0.006 0.001 HIS A1542 PHE 0.017 0.001 PHE A 100 TYR 0.018 0.001 TYR A1739 ARG 0.004 0.000 ARG A1616 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 7) link_NAG-ASN : angle 1.61383 ( 21) link_BETA1-4 : bond 0.00784 ( 2) link_BETA1-4 : angle 4.09671 ( 6) hydrogen bonds : bond 0.03823 ( 777) hydrogen bonds : angle 4.56571 ( 2232) SS BOND : bond 0.00472 ( 11) SS BOND : angle 1.15982 ( 22) covalent geometry : bond 0.00399 (12787) covalent geometry : angle 0.61541 (17317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 238 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7908 (m-80) cc_final: 0.7622 (m-80) REVERT: A 135 THR cc_start: 0.8712 (m) cc_final: 0.8506 (t) REVERT: A 147 ASN cc_start: 0.8132 (t0) cc_final: 0.7824 (t0) REVERT: A 151 TRP cc_start: 0.7309 (p-90) cc_final: 0.6999 (p90) REVERT: A 156 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6626 (pt0) REVERT: A 170 LYS cc_start: 0.7498 (ttmt) cc_final: 0.7286 (mtpt) REVERT: A 240 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6487 (mp10) REVERT: A 358 MET cc_start: 0.8821 (tmt) cc_final: 0.8611 (ttt) REVERT: A 406 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7288 (tm-30) REVERT: A 407 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6958 (mm-30) REVERT: A 408 GLN cc_start: 0.7195 (tp40) cc_final: 0.6201 (pt0) REVERT: A 773 LYS cc_start: 0.8586 (tptp) cc_final: 0.8030 (ttmt) REVERT: A 1188 ILE cc_start: 0.8561 (mm) cc_final: 0.8260 (mm) REVERT: A 1195 GLU cc_start: 0.7481 (tp30) cc_final: 0.7267 (tp30) REVERT: A 1196 SER cc_start: 0.8538 (t) cc_final: 0.8198 (m) REVERT: A 1251 LYS cc_start: 0.7901 (tttt) cc_final: 0.7274 (pttm) REVERT: A 1305 GLU cc_start: 0.7109 (pm20) cc_final: 0.5775 (tt0) REVERT: A 1331 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7738 (t80) REVERT: A 1452 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.5794 (m-10) REVERT: A 1524 LEU cc_start: 0.8434 (mm) cc_final: 0.8218 (mm) REVERT: A 1543 MET cc_start: 0.8708 (ttt) cc_final: 0.8484 (ttt) REVERT: A 1579 ASN cc_start: 0.8724 (m110) cc_final: 0.8391 (m-40) REVERT: A 1609 PHE cc_start: 0.8063 (t80) cc_final: 0.7773 (t80) REVERT: A 1754 MET cc_start: 0.8666 (mtt) cc_final: 0.8391 (mtt) REVERT: B 62 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7936 (ttpt) REVERT: B 154 MET cc_start: 0.7113 (ttp) cc_final: 0.6816 (tmm) REVERT: B 178 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7084 (tmm) REVERT: B 182 TYR cc_start: 0.8575 (t80) cc_final: 0.8067 (t80) REVERT: C 85 MET cc_start: 0.5789 (mmm) cc_final: 0.5485 (mmt) outliers start: 66 outliers final: 52 residues processed: 283 average time/residue: 0.2106 time to fit residues: 91.4020 Evaluate side-chains 289 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1455 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1559 THR Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1677 ASP Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 61 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 146 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN B 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.190326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121195 restraints weight = 14606.721| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.08 r_work: 0.3161 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12807 Z= 0.152 Angle : 0.614 10.577 17366 Z= 0.306 Chirality : 0.042 0.292 1997 Planarity : 0.004 0.037 2116 Dihedral : 8.270 87.869 1911 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 4.92 % Allowed : 23.04 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1509 helix: 1.68 (0.17), residues: 852 sheet: -0.64 (0.40), residues: 142 loop : -0.94 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1408 HIS 0.004 0.001 HIS A1542 PHE 0.018 0.001 PHE A 100 TYR 0.021 0.001 TYR A1548 ARG 0.002 0.000 ARG A1616 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 7) link_NAG-ASN : angle 1.54037 ( 21) link_BETA1-4 : bond 0.00770 ( 2) link_BETA1-4 : angle 4.11197 ( 6) hydrogen bonds : bond 0.03754 ( 777) hydrogen bonds : angle 4.54400 ( 2232) SS BOND : bond 0.00449 ( 11) SS BOND : angle 1.51470 ( 22) covalent geometry : bond 0.00347 (12787) covalent geometry : angle 0.60530 (17317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 238 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7914 (m-80) cc_final: 0.7646 (m-80) REVERT: A 151 TRP cc_start: 0.7289 (p-90) cc_final: 0.6988 (p90) REVERT: A 156 GLU cc_start: 0.7670 (mm-30) cc_final: 0.6625 (pt0) REVERT: A 240 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6573 (mp10) REVERT: A 358 MET cc_start: 0.8779 (tmt) cc_final: 0.8573 (ttt) REVERT: A 379 MET cc_start: 0.8333 (tmm) cc_final: 0.7964 (tmm) REVERT: A 408 GLN cc_start: 0.7186 (tp40) cc_final: 0.6182 (pt0) REVERT: A 773 LYS cc_start: 0.8579 (tptp) cc_final: 0.8006 (ttmt) REVERT: A 1188 ILE cc_start: 0.8560 (mm) cc_final: 0.8257 (mm) REVERT: A 1195 GLU cc_start: 0.7481 (tp30) cc_final: 0.7273 (tp30) REVERT: A 1196 SER cc_start: 0.8545 (t) cc_final: 0.8197 (m) REVERT: A 1251 LYS cc_start: 0.7875 (tttt) cc_final: 0.7304 (pttm) REVERT: A 1305 GLU cc_start: 0.7017 (pm20) cc_final: 0.5682 (tt0) REVERT: A 1331 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7794 (t80) REVERT: A 1452 PHE cc_start: 0.6311 (OUTLIER) cc_final: 0.5797 (m-10) REVERT: A 1462 GLN cc_start: 0.7373 (tt0) cc_final: 0.6853 (mt0) REVERT: A 1543 MET cc_start: 0.8723 (ttt) cc_final: 0.8483 (ttt) REVERT: A 1579 ASN cc_start: 0.8724 (m110) cc_final: 0.8402 (m-40) REVERT: A 1609 PHE cc_start: 0.8042 (t80) cc_final: 0.7771 (t80) REVERT: A 1753 ASN cc_start: 0.9024 (m-40) cc_final: 0.8814 (m-40) REVERT: A 1754 MET cc_start: 0.8644 (mtt) cc_final: 0.8402 (mtt) REVERT: B 62 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7948 (ttpt) REVERT: B 80 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8430 (mt) REVERT: B 154 MET cc_start: 0.7084 (ttp) cc_final: 0.6784 (tmm) REVERT: B 178 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7062 (tmm) REVERT: B 182 TYR cc_start: 0.8593 (t80) cc_final: 0.8090 (t80) REVERT: C 85 MET cc_start: 0.5841 (mmm) cc_final: 0.5540 (mmt) outliers start: 67 outliers final: 56 residues processed: 286 average time/residue: 0.2147 time to fit residues: 93.5263 Evaluate side-chains 291 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1191 HIS Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1455 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1677 ASP Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 chunk 26 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 90 optimal weight: 0.1980 chunk 147 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A1379 ASN A1505 GLN B 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.192427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123889 restraints weight = 14652.830| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.13 r_work: 0.3156 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 12807 Z= 0.118 Angle : 0.597 10.815 17366 Z= 0.297 Chirality : 0.042 0.320 1997 Planarity : 0.004 0.035 2116 Dihedral : 8.064 85.183 1911 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 3.74 % Allowed : 24.50 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1509 helix: 1.79 (0.18), residues: 853 sheet: -0.51 (0.42), residues: 136 loop : -0.84 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1408 HIS 0.004 0.001 HIS A1542 PHE 0.022 0.001 PHE A 100 TYR 0.014 0.001 TYR A1739 ARG 0.002 0.000 ARG A1616 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 7) link_NAG-ASN : angle 1.36208 ( 21) link_BETA1-4 : bond 0.00790 ( 2) link_BETA1-4 : angle 4.09765 ( 6) hydrogen bonds : bond 0.03641 ( 777) hydrogen bonds : angle 4.48076 ( 2232) SS BOND : bond 0.00346 ( 11) SS BOND : angle 1.31170 ( 22) covalent geometry : bond 0.00249 (12787) covalent geometry : angle 0.58940 (17317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7832 (m-80) cc_final: 0.7618 (m-80) REVERT: A 151 TRP cc_start: 0.7244 (p-90) cc_final: 0.6942 (p90) REVERT: A 156 GLU cc_start: 0.7645 (mm-30) cc_final: 0.6615 (pt0) REVERT: A 240 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6480 (mp10) REVERT: A 379 MET cc_start: 0.8127 (tmm) cc_final: 0.7799 (tmm) REVERT: A 408 GLN cc_start: 0.7150 (tp40) cc_final: 0.6161 (pt0) REVERT: A 773 LYS cc_start: 0.8550 (tptp) cc_final: 0.7978 (ttmt) REVERT: A 1188 ILE cc_start: 0.8520 (mm) cc_final: 0.8212 (mm) REVERT: A 1196 SER cc_start: 0.8497 (t) cc_final: 0.8158 (m) REVERT: A 1251 LYS cc_start: 0.7776 (tttt) cc_final: 0.7262 (pttm) REVERT: A 1305 GLU cc_start: 0.6924 (pm20) cc_final: 0.5637 (tt0) REVERT: A 1331 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7816 (t80) REVERT: A 1452 PHE cc_start: 0.6440 (OUTLIER) cc_final: 0.5931 (m-10) REVERT: A 1462 GLN cc_start: 0.7337 (tt0) cc_final: 0.6822 (mt0) REVERT: A 1543 MET cc_start: 0.8685 (ttt) cc_final: 0.8443 (ttt) REVERT: A 1579 ASN cc_start: 0.8731 (m110) cc_final: 0.8417 (m-40) REVERT: A 1609 PHE cc_start: 0.8021 (t80) cc_final: 0.7757 (t80) REVERT: A 1613 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7416 (mtp180) REVERT: A 1753 ASN cc_start: 0.9004 (m-40) cc_final: 0.8733 (m110) REVERT: A 1754 MET cc_start: 0.8532 (mtt) cc_final: 0.8304 (mtt) REVERT: B 62 LYS cc_start: 0.8425 (ttmt) cc_final: 0.7998 (ttpt) REVERT: B 80 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8428 (mt) REVERT: B 154 MET cc_start: 0.7261 (ttp) cc_final: 0.6973 (tmm) REVERT: B 178 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7037 (tmm) REVERT: B 182 TYR cc_start: 0.8595 (t80) cc_final: 0.8100 (t80) REVERT: C 85 MET cc_start: 0.6003 (mmm) cc_final: 0.5723 (mmt) outliers start: 51 outliers final: 42 residues processed: 278 average time/residue: 0.2110 time to fit residues: 89.6515 Evaluate side-chains 279 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1191 HIS Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1455 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 127 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 12 optimal weight: 0.0020 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A1505 GLN B 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.192488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123964 restraints weight = 14637.309| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.14 r_work: 0.3171 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12807 Z= 0.122 Angle : 0.605 11.026 17366 Z= 0.299 Chirality : 0.042 0.334 1997 Planarity : 0.004 0.035 2116 Dihedral : 7.886 82.211 1911 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 3.37 % Allowed : 25.24 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.22), residues: 1509 helix: 1.82 (0.17), residues: 853 sheet: -0.56 (0.41), residues: 142 loop : -0.82 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1408 HIS 0.004 0.001 HIS A1542 PHE 0.024 0.001 PHE A 100 TYR 0.014 0.001 TYR A1739 ARG 0.002 0.000 ARG A1616 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 7) link_NAG-ASN : angle 1.31613 ( 21) link_BETA1-4 : bond 0.00896 ( 2) link_BETA1-4 : angle 4.21471 ( 6) hydrogen bonds : bond 0.03596 ( 777) hydrogen bonds : angle 4.46266 ( 2232) SS BOND : bond 0.00337 ( 11) SS BOND : angle 1.20687 ( 22) covalent geometry : bond 0.00263 (12787) covalent geometry : angle 0.59731 (17317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9059.57 seconds wall clock time: 154 minutes 50.23 seconds (9290.23 seconds total)