Starting phenix.real_space_refine on Mon Dec 30 17:56:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xm9_33292/12_2024/7xm9_33292_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xm9_33292/12_2024/7xm9_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_33292/12_2024/7xm9_33292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xm9_33292/12_2024/7xm9_33292.map" model { file = "/net/cci-nas-00/data/ceres_data/7xm9_33292/12_2024/7xm9_33292_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xm9_33292/12_2024/7xm9_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.57, per 1000 atoms: 0.61 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: 3.04 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: 1.23 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: 4.40 Time building geometry restraints manager: 3.54 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.110 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.290 ------------------------------------------------------------------------------- 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 : 0.007 0.223 12787 Z= 0.474 Angle : 0.856 19.886 17317 Z= 0.483 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 *********************** 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 : 1.652 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: 0.2469 time to fit residues: 128.5553 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 : 1.346 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 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 12787 Z= 0.198 Angle : 0.655 9.995 17317 Z= 0.331 Chirality : 0.043 0.261 1997 Planarity : 0.005 0.051 2116 Dihedral : 10.898 100.311 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 *********************** 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 : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7977 (m-80) cc_final: 0.7493 (m-80) REVERT: A 145 MET cc_start: 0.8406 (mmm) cc_final: 0.8160 (mmm) REVERT: A 151 TRP cc_start: 0.7449 (p-90) cc_final: 0.6981 (p90) REVERT: A 156 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6794 (pt0) REVERT: A 216 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8111 (t80) REVERT: A 217 ARG cc_start: 0.7930 (ptp-110) cc_final: 0.7289 (mtm-85) REVERT: A 240 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6473 (mp10) REVERT: A 289 ILE cc_start: 0.9183 (mm) cc_final: 0.8968 (mm) REVERT: A 364 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: A 398 LEU cc_start: 0.8238 (mp) cc_final: 0.8031 (mp) REVERT: A 408 GLN cc_start: 0.7452 (tp40) cc_final: 0.7154 (tp40) REVERT: A 761 MET cc_start: 0.8227 (ttm) cc_final: 0.7930 (mtp) REVERT: A 773 LYS cc_start: 0.8653 (tptp) cc_final: 0.8213 (ttmt) REVERT: A 774 ASN cc_start: 0.7646 (m-40) cc_final: 0.7433 (m110) REVERT: A 948 TYR cc_start: 0.7997 (m-80) cc_final: 0.7557 (m-80) REVERT: A 1188 ILE cc_start: 0.8804 (mm) cc_final: 0.8510 (mm) REVERT: A 1196 SER cc_start: 0.8384 (t) cc_final: 0.8052 (m) REVERT: A 1251 LYS cc_start: 0.7965 (tttt) cc_final: 0.7648 (pttm) REVERT: A 1252 THR cc_start: 0.8996 (m) cc_final: 0.8726 (p) REVERT: A 1331 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7276 (t80) REVERT: A 1481 TYR cc_start: 0.7198 (m-80) cc_final: 0.6935 (m-10) REVERT: A 1515 GLN cc_start: 0.7877 (pt0) cc_final: 0.7674 (pt0) REVERT: A 1524 LEU cc_start: 0.8364 (mm) cc_final: 0.8109 (mm) REVERT: A 1542 HIS cc_start: 0.7539 (t70) cc_final: 0.7290 (t-170) REVERT: A 1609 PHE cc_start: 0.8144 (t80) cc_final: 0.7725 (t80) REVERT: B 62 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7813 (ttpt) REVERT: B 119 TYR cc_start: 0.8764 (m-80) cc_final: 0.8535 (m-80) REVERT: B 120 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7222 (mm-30) REVERT: B 152 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7065 (mtp85) REVERT: B 178 MET cc_start: 0.7959 (mtt) cc_final: 0.7210 (tmm) REVERT: B 182 TYR cc_start: 0.8445 (t80) cc_final: 0.8199 (t80) REVERT: C 85 MET cc_start: 0.3454 (OUTLIER) cc_final: 0.3240 (mmt) outliers start: 54 outliers final: 29 residues processed: 315 average time/residue: 0.2391 time to fit residues: 110.8639 Evaluate side-chains 288 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 76 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 123 optimal weight: 0.2980 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** A1753 ASN B 102 GLN B 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12787 Z= 0.225 Angle : 0.613 9.521 17317 Z= 0.311 Chirality : 0.042 0.266 1997 Planarity : 0.004 0.046 2116 Dihedral : 9.733 97.214 1918 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.26 % Allowed : 20.54 % Favored : 75.20 % 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: 0.13 (0.21), residues: 1509 helix: 1.15 (0.17), residues: 849 sheet: -1.14 (0.40), residues: 139 loop : -1.29 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1700 HIS 0.003 0.001 HIS A 273 PHE 0.018 0.001 PHE A 159 TYR 0.016 0.001 TYR A1739 ARG 0.003 0.000 ARG B 89 *********************** 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 318 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.8051 (m-80) cc_final: 0.7624 (m-80) REVERT: A 145 MET cc_start: 0.8279 (mmm) cc_final: 0.7963 (mmm) REVERT: A 151 TRP cc_start: 0.7478 (p-90) cc_final: 0.7046 (p90) REVERT: A 156 GLU cc_start: 0.7815 (mm-30) cc_final: 0.6904 (pt0) REVERT: A 216 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8118 (t80) REVERT: A 217 ARG cc_start: 0.7916 (ptp-110) cc_final: 0.7198 (mtm-85) REVERT: A 240 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6456 (mp10) REVERT: A 288 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8786 (p) REVERT: A 364 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: A 398 LEU cc_start: 0.8321 (mp) cc_final: 0.8110 (mp) REVERT: A 408 GLN cc_start: 0.7397 (tp40) cc_final: 0.6277 (pt0) REVERT: A 761 MET cc_start: 0.8327 (ttm) cc_final: 0.8048 (mtp) REVERT: A 773 LYS cc_start: 0.8644 (tptp) cc_final: 0.8213 (ttmt) REVERT: A 948 TYR cc_start: 0.8123 (m-80) cc_final: 0.7524 (m-80) REVERT: A 1188 ILE cc_start: 0.8760 (mm) cc_final: 0.8457 (mm) REVERT: A 1196 SER cc_start: 0.8587 (t) cc_final: 0.8234 (m) REVERT: A 1251 LYS cc_start: 0.7896 (tttt) cc_final: 0.7506 (pttm) REVERT: A 1252 THR cc_start: 0.9052 (m) cc_final: 0.8712 (p) REVERT: A 1305 GLU cc_start: 0.6864 (pm20) cc_final: 0.6582 (pm20) REVERT: A 1331 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7431 (t80) REVERT: A 1609 PHE cc_start: 0.8225 (t80) cc_final: 0.7784 (t80) REVERT: A 1613 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7708 (mtp180) REVERT: A 1754 MET cc_start: 0.8433 (mtt) cc_final: 0.8202 (mtt) REVERT: B 62 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7877 (ttpt) REVERT: B 120 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7336 (mm-30) REVERT: B 152 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7143 (ttp80) REVERT: B 178 MET cc_start: 0.8093 (mtt) cc_final: 0.7298 (tmm) outliers start: 58 outliers final: 32 residues processed: 300 average time/residue: 0.2149 time to fit residues: 96.7840 Evaluate side-chains 285 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 216 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 288 SER 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 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.0370 chunk 103 optimal weight: 0.2980 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 overall best weight: 1.0262 ------------------------------------------------------------------------------- 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 A 774 ASN A 809 ASN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN A1528 ASN A1753 ASN C 82 GLN C 104 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12787 Z= 0.211 Angle : 0.596 9.792 17317 Z= 0.301 Chirality : 0.042 0.265 1997 Planarity : 0.004 0.040 2116 Dihedral : 9.233 95.063 1915 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.40 % Allowed : 21.35 % Favored : 74.25 % 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: 0.41 (0.21), residues: 1509 helix: 1.34 (0.17), residues: 855 sheet: -0.95 (0.41), residues: 139 loop : -1.15 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1408 HIS 0.009 0.001 HIS A1542 PHE 0.013 0.001 PHE A1440 TYR 0.019 0.001 TYR A1548 ARG 0.002 0.000 ARG A1631 *********************** 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 312 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 252 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7982 (m-80) cc_final: 0.7680 (m-80) REVERT: A 151 TRP cc_start: 0.7523 (p-90) cc_final: 0.7119 (p90) REVERT: A 156 GLU cc_start: 0.7819 (mm-30) cc_final: 0.6898 (pt0) REVERT: A 216 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8146 (t80) REVERT: A 217 ARG cc_start: 0.7900 (ptp-110) cc_final: 0.7189 (mtm-85) REVERT: A 240 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6502 (mp10) REVERT: A 364 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: A 408 GLN cc_start: 0.7301 (tp40) cc_final: 0.6289 (pt0) REVERT: A 761 MET cc_start: 0.8347 (ttm) cc_final: 0.7937 (mtp) REVERT: A 773 LYS cc_start: 0.8607 (tptp) cc_final: 0.8166 (ttmt) REVERT: A 948 TYR cc_start: 0.8172 (m-80) cc_final: 0.7470 (m-80) REVERT: A 1188 ILE cc_start: 0.8723 (mm) cc_final: 0.8409 (mm) REVERT: A 1196 SER cc_start: 0.8620 (t) cc_final: 0.8279 (m) REVERT: A 1251 LYS cc_start: 0.8106 (tttt) cc_final: 0.7776 (pttm) REVERT: A 1305 GLU cc_start: 0.6982 (pm20) cc_final: 0.6645 (pm20) REVERT: A 1331 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7519 (t80) REVERT: A 1524 LEU cc_start: 0.8486 (mm) cc_final: 0.8206 (mm) REVERT: A 1579 ASN cc_start: 0.8628 (m110) cc_final: 0.8242 (m-40) REVERT: A 1609 PHE cc_start: 0.8231 (t80) cc_final: 0.7832 (t80) REVERT: A 1613 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7656 (mtp180) REVERT: A 1753 ASN cc_start: 0.8418 (m-40) cc_final: 0.8215 (m-40) REVERT: A 1754 MET cc_start: 0.8375 (mtt) cc_final: 0.8149 (mtt) REVERT: B 62 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7855 (ttpt) REVERT: B 119 TYR cc_start: 0.8806 (m-80) cc_final: 0.8515 (m-80) REVERT: B 120 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7295 (mm-30) REVERT: B 152 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7131 (ttp80) REVERT: B 178 MET cc_start: 0.8070 (mtt) cc_final: 0.7172 (tmm) outliers start: 60 outliers final: 40 residues processed: 293 average time/residue: 0.2186 time to fit residues: 95.8649 Evaluate side-chains 286 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU 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 242 VAL 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 753 CYS 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 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 1238 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 1508 ILE Chi-restraints excluded: chain A residue 1557 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 774 ASN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12787 Z= 0.196 Angle : 0.588 9.796 17317 Z= 0.296 Chirality : 0.041 0.265 1997 Planarity : 0.004 0.037 2116 Dihedral : 9.040 94.223 1915 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.18 % Allowed : 22.16 % 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: 0.56 (0.21), residues: 1509 helix: 1.45 (0.17), residues: 861 sheet: -0.80 (0.42), residues: 139 loop : -1.12 (0.27), residues: 509 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 0.001 PHE A1574 TYR 0.017 0.001 TYR A1739 ARG 0.002 0.000 ARG A1631 *********************** 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 303 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.8038 (m-80) cc_final: 0.7747 (m-80) REVERT: A 151 TRP cc_start: 0.7567 (p-90) cc_final: 0.7164 (p90) REVERT: A 156 GLU cc_start: 0.7786 (mm-30) cc_final: 0.6896 (pt0) REVERT: A 216 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8146 (t80) REVERT: A 217 ARG cc_start: 0.7906 (ptp-110) cc_final: 0.7152 (mtm-85) REVERT: A 240 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6499 (mp10) REVERT: A 406 GLU cc_start: 0.6125 (tm-30) cc_final: 0.5670 (tm-30) REVERT: A 408 GLN cc_start: 0.7349 (tp40) cc_final: 0.6339 (pt0) REVERT: A 761 MET cc_start: 0.8356 (ttm) cc_final: 0.7963 (mtp) REVERT: A 773 LYS cc_start: 0.8595 (tptp) cc_final: 0.8197 (ttmt) REVERT: A 948 TYR cc_start: 0.8164 (m-80) cc_final: 0.7523 (m-80) REVERT: A 1188 ILE cc_start: 0.8682 (mm) cc_final: 0.8357 (mm) REVERT: A 1196 SER cc_start: 0.8733 (t) cc_final: 0.8329 (m) REVERT: A 1251 LYS cc_start: 0.8166 (tttt) cc_final: 0.7769 (pttm) REVERT: A 1305 GLU cc_start: 0.7070 (pm20) cc_final: 0.6340 (tt0) REVERT: A 1331 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7567 (t80) REVERT: A 1524 LEU cc_start: 0.8515 (mm) cc_final: 0.8214 (mm) REVERT: A 1579 ASN cc_start: 0.8646 (m110) cc_final: 0.8284 (m-40) REVERT: A 1609 PHE cc_start: 0.8229 (t80) cc_final: 0.7811 (t80) REVERT: A 1613 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7667 (mtp180) REVERT: A 1753 ASN cc_start: 0.8422 (m-40) cc_final: 0.8207 (m-40) REVERT: B 62 LYS cc_start: 0.8340 (ttmt) cc_final: 0.7893 (ttpt) REVERT: B 152 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7049 (ttp80) REVERT: B 178 MET cc_start: 0.8000 (mtt) cc_final: 0.7134 (tmm) outliers start: 57 outliers final: 44 residues processed: 287 average time/residue: 0.2126 time to fit residues: 92.8288 Evaluate side-chains 281 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 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 242 VAL 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 400 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 VAL 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 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 1238 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 1508 ILE Chi-restraints excluded: chain A residue 1557 LEU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12787 Z= 0.224 Angle : 0.595 10.138 17317 Z= 0.300 Chirality : 0.042 0.268 1997 Planarity : 0.004 0.038 2116 Dihedral : 8.659 92.287 1912 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.26 % Allowed : 22.74 % Favored : 73.00 % 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: 0.62 (0.22), residues: 1509 helix: 1.47 (0.17), residues: 861 sheet: -0.72 (0.42), residues: 139 loop : -1.05 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1700 HIS 0.005 0.001 HIS A1542 PHE 0.029 0.001 PHE A 165 TYR 0.016 0.001 TYR A 367 ARG 0.002 0.000 ARG A1631 *********************** 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 303 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7975 (m-80) cc_final: 0.7667 (m-80) REVERT: A 151 TRP cc_start: 0.7600 (p-90) cc_final: 0.7181 (p90) REVERT: A 156 GLU cc_start: 0.7766 (mm-30) cc_final: 0.6758 (pt0) REVERT: A 240 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6415 (mp10) REVERT: A 406 GLU cc_start: 0.6220 (tm-30) cc_final: 0.5713 (tm-30) REVERT: A 408 GLN cc_start: 0.7403 (tp40) cc_final: 0.6405 (pt0) REVERT: A 761 MET cc_start: 0.8350 (ttm) cc_final: 0.7915 (mtp) REVERT: A 773 LYS cc_start: 0.8704 (tptp) cc_final: 0.8224 (ttmt) REVERT: A 948 TYR cc_start: 0.8193 (m-80) cc_final: 0.7628 (m-80) REVERT: A 1188 ILE cc_start: 0.8680 (mm) cc_final: 0.8358 (mm) REVERT: A 1196 SER cc_start: 0.8741 (t) cc_final: 0.8329 (m) REVERT: A 1251 LYS cc_start: 0.8169 (tttt) cc_final: 0.7772 (pttm) REVERT: A 1305 GLU cc_start: 0.7124 (pm20) cc_final: 0.6264 (tt0) REVERT: A 1331 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7541 (t80) REVERT: A 1548 TYR cc_start: 0.8681 (t80) cc_final: 0.8461 (t80) REVERT: A 1579 ASN cc_start: 0.8734 (m110) cc_final: 0.8358 (m-40) REVERT: A 1609 PHE cc_start: 0.8217 (t80) cc_final: 0.8000 (t80) REVERT: A 1613 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7706 (mtp180) REVERT: A 1753 ASN cc_start: 0.8486 (m-40) cc_final: 0.8232 (m-40) REVERT: A 1754 MET cc_start: 0.8303 (mtt) cc_final: 0.7975 (mtt) REVERT: B 62 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7894 (ttpt) REVERT: B 152 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7039 (ttp80) REVERT: B 178 MET cc_start: 0.7991 (mtt) cc_final: 0.7109 (tmm) outliers start: 58 outliers final: 48 residues processed: 288 average time/residue: 0.2127 time to fit residues: 93.2216 Evaluate side-chains 282 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 232 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 194 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 242 VAL 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 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 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 1553 VAL Chi-restraints excluded: chain A residue 1586 VAL 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 78 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 C residue 55 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12787 Z= 0.173 Angle : 0.578 10.397 17317 Z= 0.290 Chirality : 0.041 0.262 1997 Planarity : 0.004 0.037 2116 Dihedral : 8.369 89.891 1912 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.04 % Allowed : 23.62 % Favored : 72.34 % 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: 0.81 (0.22), residues: 1509 helix: 1.64 (0.17), residues: 857 sheet: -0.65 (0.41), residues: 145 loop : -0.99 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1700 HIS 0.003 0.001 HIS A1542 PHE 0.033 0.001 PHE A 165 TYR 0.015 0.001 TYR A 367 ARG 0.002 0.000 ARG A 838 *********************** 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 297 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7983 (m-80) cc_final: 0.7726 (m-80) REVERT: A 151 TRP cc_start: 0.7452 (p-90) cc_final: 0.7115 (p90) REVERT: A 156 GLU cc_start: 0.7759 (mm-30) cc_final: 0.6737 (pt0) REVERT: A 167 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8229 (p) REVERT: A 216 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8144 (t80) REVERT: A 240 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6369 (mp10) REVERT: A 358 MET cc_start: 0.8395 (tmt) cc_final: 0.8145 (ttt) REVERT: A 379 MET cc_start: 0.7625 (tmm) cc_final: 0.7271 (tmm) REVERT: A 408 GLN cc_start: 0.7385 (tp40) cc_final: 0.6426 (pt0) REVERT: A 773 LYS cc_start: 0.8792 (tptp) cc_final: 0.8269 (ttmt) REVERT: A 948 TYR cc_start: 0.8150 (m-80) cc_final: 0.7557 (m-80) REVERT: A 1188 ILE cc_start: 0.8657 (mm) cc_final: 0.8332 (mm) REVERT: A 1196 SER cc_start: 0.8750 (t) cc_final: 0.8345 (m) REVERT: A 1251 LYS cc_start: 0.8102 (tttt) cc_final: 0.7682 (pttm) REVERT: A 1305 GLU cc_start: 0.7091 (pm20) cc_final: 0.6333 (tt0) REVERT: A 1331 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7714 (t80) REVERT: A 1524 LEU cc_start: 0.8479 (mm) cc_final: 0.8245 (mm) REVERT: A 1529 MET cc_start: 0.7663 (ttt) cc_final: 0.7438 (ttt) REVERT: A 1548 TYR cc_start: 0.8716 (t80) cc_final: 0.8428 (t80) REVERT: A 1579 ASN cc_start: 0.8719 (m110) cc_final: 0.8371 (m-40) REVERT: A 1613 ARG cc_start: 0.8296 (mtp85) cc_final: 0.7746 (mtp180) REVERT: A 1753 ASN cc_start: 0.8414 (m-40) cc_final: 0.8178 (m-40) REVERT: A 1754 MET cc_start: 0.8200 (mtt) cc_final: 0.7862 (mtt) REVERT: B 62 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7948 (ttpt) REVERT: B 178 MET cc_start: 0.7987 (mtt) cc_final: 0.7080 (tmm) outliers start: 55 outliers final: 38 residues processed: 284 average time/residue: 0.2208 time to fit residues: 96.2535 Evaluate side-chains 272 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 195 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 240 GLN 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 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 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 1508 ILE Chi-restraints excluded: chain A residue 1586 VAL 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 68 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 B residue 144 ILE Chi-restraints excluded: chain B residue 157 ILE 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 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 0.0770 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12787 Z= 0.178 Angle : 0.590 10.604 17317 Z= 0.295 Chirality : 0.042 0.262 1997 Planarity : 0.004 0.037 2116 Dihedral : 8.207 87.330 1912 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.33 % Allowed : 23.48 % 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: 0.89 (0.22), residues: 1509 helix: 1.68 (0.17), residues: 857 sheet: -0.58 (0.41), residues: 145 loop : -0.92 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1700 HIS 0.003 0.000 HIS A1542 PHE 0.032 0.001 PHE A 165 TYR 0.015 0.001 TYR A1739 ARG 0.002 0.000 ARG A 838 *********************** 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 296 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7986 (m-80) cc_final: 0.7765 (m-80) REVERT: A 151 TRP cc_start: 0.7311 (p-90) cc_final: 0.7040 (p90) REVERT: A 156 GLU cc_start: 0.7758 (mm-30) cc_final: 0.6732 (pt0) REVERT: A 167 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 216 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 240 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6381 (mp10) REVERT: A 358 MET cc_start: 0.8384 (tmt) cc_final: 0.8181 (ttt) REVERT: A 379 MET cc_start: 0.7587 (tmm) cc_final: 0.7224 (tmm) REVERT: A 408 GLN cc_start: 0.7380 (tp40) cc_final: 0.6436 (pt0) REVERT: A 773 LYS cc_start: 0.8768 (tptp) cc_final: 0.8217 (ttmt) REVERT: A 854 MET cc_start: 0.6855 (ttt) cc_final: 0.6544 (ttm) REVERT: A 948 TYR cc_start: 0.8161 (m-80) cc_final: 0.7561 (m-80) REVERT: A 1188 ILE cc_start: 0.8647 (mm) cc_final: 0.8316 (mm) REVERT: A 1196 SER cc_start: 0.8757 (t) cc_final: 0.8347 (m) REVERT: A 1251 LYS cc_start: 0.8103 (tttt) cc_final: 0.7700 (pttm) REVERT: A 1305 GLU cc_start: 0.7095 (pm20) cc_final: 0.6334 (tt0) REVERT: A 1331 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7727 (t80) REVERT: A 1452 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.6088 (m-10) REVERT: A 1462 GLN cc_start: 0.7185 (tt0) cc_final: 0.6775 (mt0) REVERT: A 1548 TYR cc_start: 0.8692 (t80) cc_final: 0.8354 (t80) REVERT: A 1579 ASN cc_start: 0.8731 (m110) cc_final: 0.8362 (m-40) REVERT: A 1609 PHE cc_start: 0.8428 (t80) cc_final: 0.8105 (t80) REVERT: A 1753 ASN cc_start: 0.8437 (m-40) cc_final: 0.8209 (m-40) REVERT: A 1754 MET cc_start: 0.8211 (mtt) cc_final: 0.7848 (mtt) REVERT: B 62 LYS cc_start: 0.8376 (ttmt) cc_final: 0.7945 (ttpt) REVERT: B 178 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7065 (tmm) outliers start: 59 outliers final: 46 residues processed: 279 average time/residue: 0.2343 time to fit residues: 100.2516 Evaluate side-chains 283 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE 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 195 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 240 GLN 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 765 HIS Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 818 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 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 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 1566 LEU Chi-restraints excluded: chain A residue 1586 VAL 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 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 128 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 30.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 C 143 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12787 Z= 0.198 Angle : 0.599 10.909 17317 Z= 0.299 Chirality : 0.042 0.299 1997 Planarity : 0.004 0.036 2116 Dihedral : 8.091 83.716 1912 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 4.18 % Allowed : 23.40 % Favored : 72.41 % 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: 0.96 (0.22), residues: 1509 helix: 1.71 (0.17), residues: 857 sheet: -0.46 (0.42), residues: 136 loop : -0.86 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1408 HIS 0.003 0.001 HIS A1542 PHE 0.020 0.001 PHE A1609 TYR 0.016 0.001 TYR A1739 ARG 0.002 0.000 ARG A1616 *********************** 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 287 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 TRP cc_start: 0.7292 (p-90) cc_final: 0.7034 (p90) REVERT: A 156 GLU cc_start: 0.7713 (mm-30) cc_final: 0.6698 (pt0) REVERT: A 240 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6446 (mp10) REVERT: A 358 MET cc_start: 0.8404 (tmt) cc_final: 0.8195 (ttt) REVERT: A 379 MET cc_start: 0.7594 (tmm) cc_final: 0.7199 (tmm) REVERT: A 408 GLN cc_start: 0.7409 (tp40) cc_final: 0.6457 (pt0) REVERT: A 773 LYS cc_start: 0.8836 (tptp) cc_final: 0.8288 (ttmt) REVERT: A 948 TYR cc_start: 0.8170 (m-80) cc_final: 0.7576 (m-80) REVERT: A 1188 ILE cc_start: 0.8594 (mm) cc_final: 0.8266 (mm) REVERT: A 1196 SER cc_start: 0.8761 (t) cc_final: 0.8353 (m) REVERT: A 1251 LYS cc_start: 0.8095 (tttt) cc_final: 0.7686 (pttm) REVERT: A 1305 GLU cc_start: 0.6990 (pm20) cc_final: 0.6198 (tt0) REVERT: A 1331 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7660 (t80) REVERT: A 1452 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.6027 (m-10) REVERT: A 1462 GLN cc_start: 0.7193 (tt0) cc_final: 0.6790 (mt0) REVERT: A 1524 LEU cc_start: 0.8543 (mm) cc_final: 0.8315 (mm) REVERT: A 1548 TYR cc_start: 0.8693 (t80) cc_final: 0.8336 (t80) REVERT: A 1579 ASN cc_start: 0.8725 (m110) cc_final: 0.8397 (m-40) REVERT: A 1609 PHE cc_start: 0.8409 (t80) cc_final: 0.8028 (t80) REVERT: A 1753 ASN cc_start: 0.8447 (m-40) cc_final: 0.8224 (m-40) REVERT: A 1754 MET cc_start: 0.8232 (mtt) cc_final: 0.7913 (mtt) REVERT: B 62 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7948 (ttpt) REVERT: B 178 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7061 (tmm) outliers start: 57 outliers final: 51 residues processed: 272 average time/residue: 0.2140 time to fit residues: 89.0150 Evaluate side-chains 279 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 MET 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 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 818 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 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 1452 PHE Chi-restraints excluded: chain A residue 1455 VAL Chi-restraints excluded: chain A residue 1505 GLN Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1586 VAL 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 68 VAL 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 88 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12787 Z= 0.217 Angle : 0.607 11.116 17317 Z= 0.302 Chirality : 0.042 0.290 1997 Planarity : 0.004 0.035 2116 Dihedral : 7.996 80.599 1912 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 4.26 % Allowed : 23.40 % Favored : 72.34 % 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: 0.97 (0.22), residues: 1509 helix: 1.71 (0.17), residues: 857 sheet: -0.41 (0.42), residues: 136 loop : -0.85 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1408 HIS 0.003 0.001 HIS A1542 PHE 0.033 0.001 PHE A 165 TYR 0.017 0.001 TYR A1739 ARG 0.002 0.000 ARG A1616 ********************** 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 284 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 TRP cc_start: 0.7310 (p-90) cc_final: 0.7057 (p90) REVERT: A 156 GLU cc_start: 0.7712 (mm-30) cc_final: 0.6701 (pt0) REVERT: A 240 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6507 (mp10) REVERT: A 358 MET cc_start: 0.8415 (tmt) cc_final: 0.8198 (ttt) REVERT: A 379 MET cc_start: 0.7598 (tmm) cc_final: 0.7186 (tmm) REVERT: A 408 GLN cc_start: 0.7409 (tp40) cc_final: 0.6461 (pt0) REVERT: A 773 LYS cc_start: 0.8839 (tptp) cc_final: 0.8282 (ttmt) REVERT: A 854 MET cc_start: 0.6868 (ttt) cc_final: 0.6586 (ttm) REVERT: A 1188 ILE cc_start: 0.8598 (mm) cc_final: 0.8267 (mm) REVERT: A 1196 SER cc_start: 0.8766 (t) cc_final: 0.8360 (m) REVERT: A 1251 LYS cc_start: 0.8107 (tttt) cc_final: 0.7676 (pttm) REVERT: A 1305 GLU cc_start: 0.7007 (pm20) cc_final: 0.6158 (tt0) REVERT: A 1331 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7686 (t80) REVERT: A 1452 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.6139 (m-10) REVERT: A 1462 GLN cc_start: 0.7189 (tt0) cc_final: 0.6778 (mt0) REVERT: A 1524 LEU cc_start: 0.8568 (mm) cc_final: 0.8305 (mm) REVERT: A 1529 MET cc_start: 0.7689 (ttt) cc_final: 0.7476 (ttt) REVERT: A 1579 ASN cc_start: 0.8745 (m110) cc_final: 0.8415 (m-40) REVERT: A 1609 PHE cc_start: 0.8409 (t80) cc_final: 0.7996 (t80) REVERT: A 1754 MET cc_start: 0.8244 (mtt) cc_final: 0.7929 (mtt) REVERT: B 62 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7949 (ttpt) REVERT: B 178 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7055 (tmm) outliers start: 58 outliers final: 49 residues processed: 267 average time/residue: 0.2022 time to fit residues: 82.5878 Evaluate side-chains 276 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 MET 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 242 VAL Chi-restraints excluded: chain A residue 249 MET 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 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 818 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 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 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 1566 LEU Chi-restraints excluded: chain A residue 1586 VAL 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 68 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 136 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 157 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 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 A1753 ASN B 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.191790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.122034 restraints weight = 14656.924| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.16 r_work: 0.3209 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12787 Z= 0.195 Angle : 0.603 11.341 17317 Z= 0.300 Chirality : 0.042 0.288 1997 Planarity : 0.004 0.034 2116 Dihedral : 7.807 74.508 1912 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 3.89 % Allowed : 23.99 % Favored : 72.12 % 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: 1.75 (0.17), residues: 858 sheet: -0.43 (0.42), residues: 137 loop : -0.83 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1408 HIS 0.003 0.001 HIS A1542 PHE 0.021 0.001 PHE A 100 TYR 0.015 0.001 TYR A1739 ARG 0.002 0.000 ARG A1616 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3055.87 seconds wall clock time: 55 minutes 59.79 seconds (3359.79 seconds total)