Starting phenix.real_space_refine on Fri Jul 3 06:19:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xmg_33296/07_2026/7xmg_33296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmg_33296/07_2026/7xmg_33296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xmg_33296/07_2026/7xmg_33296.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xmg_33296/07_2026/7xmg_33296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xmg_33296/07_2026/7xmg_33296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmg_33296/07_2026/7xmg_33296.map" model { file = "/net/cci-nas-00/data/ceres_data/7xmg_33296/07_2026/7xmg_33296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmg_33296/07_2026/7xmg_33296.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.094 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 924 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 S 96 5.16 5 C 7679 2.51 5 N 1847 2.21 5 O 2067 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11692 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 9175 Classifications: {'peptide': 1138} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1106} Chain breaks: 3 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: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 30 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 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 chiralities: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'G4I': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 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 chiralities: 4 Time building chain proxies: 2.49, per 1000 atoms: 0.21 Number of scatterers: 11692 At special positions: 0 Unit cell: (128.96, 138.32, 114.4, 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 96 16.00 F 3 9.00 O 2067 8.00 N 1847 7.00 C 7679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.05 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS F 55 " distance=2.27 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.02 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.70 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 127 " distance=2.57 Simple disulfide: pdb=" SG CYS F 72 " - pdb=" SG CYS F 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: 0.87 Conformation dependent library (CDL) restraints added in 472.0 milliseconds 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2710 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 66.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.847A pdb=" N ILE A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 152 through 175 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.857A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 268 removed outlier: 3.604A pdb=" N LYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.461A 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 303 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: 3.798A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 414 removed outlier: 5.529A 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: 3.693A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 805 Processing helix chain 'A' and resid 806 through 821 Processing helix chain 'A' and resid 838 through 848 removed outlier: 3.601A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 864 removed outlier: 3.786A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.514A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.120A 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: 4.004A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 957 Processing helix chain 'A' and resid 958 through 973 removed outlier: 4.001A pdb=" N LEU A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 4.070A 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: 4.347A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1249 removed outlier: 3.748A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1284 through 1292 removed outlier: 3.555A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 3.624A 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: 3.668A 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 1407 through 1418 removed outlier: 4.222A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1443 removed outlier: 3.913A pdb=" N TYR A1436 " --> pdb=" O TYR A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1467 Processing helix chain 'A' and resid 1475 through 1487 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 1569 Processing helix chain 'A' and resid 1572 through 1575 removed outlier: 3.590A pdb=" N THR A1575 " --> pdb=" O TYR A1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1572 through 1575' Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1617 through 1622 Processing helix chain 'A' and resid 1623 through 1626 Processing helix chain 'A' and resid 1627 through 1666 removed outlier: 4.561A 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: 4.003A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1708 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1732 through 1768 Processing helix chain 'B' and resid 153 through 190 Processing helix chain 'F' and resid 92 through 96 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA2, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.589A pdb=" N GLN B 79 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 31 through 33 removed outlier: 4.127A pdb=" N GLU F 31 " --> pdb=" O ASN F 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.302A pdb=" N LEU F 38 " --> pdb=" O GLN F 145 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 81 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR F 69 " --> pdb=" O MET F 79 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N MET F 79 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 46 through 48 746 hydrogen bonds defined for protein. 2145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 3547 1.35 - 1.51: 3991 1.51 - 1.68: 4273 1.68 - 1.84: 152 1.84 - 2.01: 2 Bond restraints: 11965 Sorted by residual: bond pdb=" C21 G4I A2302 " pdb=" N10 G4I A2302 " ideal model delta sigma weight residual 1.279 1.467 -0.188 2.00e-02 2.50e+03 8.84e+01 bond pdb=" C36 G4I A2302 " pdb=" N12 G4I A2302 " ideal model delta sigma weight residual 1.264 1.440 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C36 G4I A2302 " pdb=" O06 G4I A2302 " ideal model delta sigma weight residual 1.340 1.184 0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C18 G4I A2302 " pdb=" N07 G4I A2302 " ideal model delta sigma weight residual 1.334 1.467 -0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" CB CYS F 127 " pdb=" SG CYS F 127 " ideal model delta sigma weight residual 1.808 2.006 -0.198 3.30e-02 9.18e+02 3.60e+01 ... (remaining 11960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 15987 2.83 - 5.66: 196 5.66 - 8.49: 22 8.49 - 11.32: 4 11.32 - 14.14: 5 Bond angle restraints: 16214 Sorted by residual: angle pdb=" C ASN F 131 " pdb=" N PRO F 132 " pdb=" CA PRO F 132 " ideal model delta sigma weight residual 119.66 114.10 5.56 7.20e-01 1.93e+00 5.97e+01 angle pdb=" C MET F 85 " pdb=" CA MET F 85 " pdb=" CB MET F 85 " ideal model delta sigma weight residual 110.42 97.76 12.66 1.99e+00 2.53e-01 4.05e+01 angle pdb=" CA CYS F 127 " pdb=" CB CYS F 127 " pdb=" SG CYS F 127 " ideal model delta sigma weight residual 114.40 128.22 -13.82 2.30e+00 1.89e-01 3.61e+01 angle pdb=" O PRO F 132 " pdb=" C PRO F 132 " pdb=" N PRO F 133 " ideal model delta sigma weight residual 121.15 123.83 -2.68 4.70e-01 4.53e+00 3.24e+01 angle pdb=" N GLN F 62 " pdb=" CA GLN F 62 " pdb=" C GLN F 62 " ideal model delta sigma weight residual 111.36 116.94 -5.58 1.09e+00 8.42e-01 2.62e+01 ... (remaining 16209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6089 17.93 - 35.86: 686 35.86 - 53.78: 159 53.78 - 71.71: 30 71.71 - 89.64: 21 Dihedral angle restraints: 6985 sinusoidal: 2791 harmonic: 4194 Sorted by residual: dihedral pdb=" CB CYS A 895 " pdb=" SG CYS A 895 " pdb=" SG CYS F 55 " pdb=" CB CYS F 55 " ideal model delta sinusoidal sigma weight residual -86.00 -2.24 -83.76 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual -86.00 -166.79 80.79 1 1.00e+01 1.00e-02 8.06e+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 -165.63 79.63 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 6982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1535 0.062 - 0.123: 308 0.123 - 0.185: 33 0.185 - 0.246: 7 0.246 - 0.308: 3 Chirality restraints: 1886 Sorted by residual: chirality pdb=" C1 NAG B 504 " pdb=" ND2 ASN B 135 " pdb=" C2 NAG B 504 " pdb=" O5 NAG B 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA ASP A1673 " pdb=" N ASP A1673 " pdb=" C ASP A1673 " pdb=" CB ASP A1673 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA PHE F 80 " pdb=" N PHE F 80 " pdb=" C PHE F 80 " pdb=" CB PHE F 80 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1883 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 G4I A2302 " 0.246 2.00e-02 2.50e+03 2.16e-01 1.28e+03 pdb=" C17 G4I A2302 " -0.501 2.00e-02 2.50e+03 pdb=" C18 G4I A2302 " 0.096 2.00e-02 2.50e+03 pdb=" C21 G4I A2302 " -0.107 2.00e-02 2.50e+03 pdb=" C24 G4I A2302 " 0.153 2.00e-02 2.50e+03 pdb=" C27 G4I A2302 " 0.110 2.00e-02 2.50e+03 pdb=" N07 G4I A2302 " 0.146 2.00e-02 2.50e+03 pdb=" N08 G4I A2302 " -0.060 2.00e-02 2.50e+03 pdb=" N09 G4I A2302 " 0.201 2.00e-02 2.50e+03 pdb=" N10 G4I A2302 " -0.280 2.00e-02 2.50e+03 pdb=" N11 G4I A2302 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 104 " 0.061 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO F 105 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO F 105 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 105 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1218 " 0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ARG A1218 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG A1218 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS A1219 " 0.019 2.00e-02 2.50e+03 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 115 2.59 - 3.17: 10553 3.17 - 3.75: 18384 3.75 - 4.32: 25724 4.32 - 4.90: 41607 Nonbonded interactions: 96383 Sorted by model distance: nonbonded pdb=" O GLY A1444 " pdb=" OG1 THR A1448 " model vdw 2.017 3.040 nonbonded pdb=" O PHE A1738 " pdb=" OG SER A1742 " model vdw 2.101 3.040 nonbonded pdb=" O GLN F 62 " pdb=" CD PRO F 132 " model vdw 2.107 3.440 nonbonded pdb=" CE2 PHE F 101 " pdb=" O GLY F 103 " model vdw 2.108 3.340 nonbonded pdb=" O TRP A1332 " pdb=" OG SER A1336 " model vdw 2.137 3.040 ... (remaining 96378 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 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 : 0.010 0.672 11983 Z= 0.509 Angle : 1.070 55.452 16259 Z= 0.565 Chirality : 0.050 0.308 1886 Planarity : 0.007 0.216 1978 Dihedral : 16.427 89.640 4248 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.33 % Favored : 92.39 % Rotamer: Outliers : 4.46 % Allowed : 19.47 % Favored : 76.08 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.19), residues: 1419 helix: -1.46 (0.15), residues: 865 sheet: -0.97 (0.49), residues: 126 loop : -2.76 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 115 TYR 0.022 0.002 TYR A1482 PHE 0.019 0.002 PHE F 80 TRP 0.018 0.002 TRP A1382 HIS 0.004 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.30 (11965) covalent geometry : angle 0.84721 / 0.47 (16214) SS BOND : bond 0.29796 / 17.97 ( 9) SS BOND : angle 19.29465 / 9.31 ( 18) hydrogen bonds : bond 0.10118 / 6.94 ( 746) hydrogen bonds : angle 4.82408 / 3.39 ( 2145) link_BETA1-4 : bond 0.00162 / 0.12 ( 2) link_BETA1-4 : angle 4.50437 / 2.41 ( 6) link_NAG-ASN : bond 0.00509 / 0.24 ( 7) link_NAG-ASN : angle 2.55441 / 1.29 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 264 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ASN cc_start: 0.7443 (p0) cc_final: 0.7226 (p0) REVERT: A 294 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5810 (tp30) REVERT: A 301 LYS cc_start: 0.7397 (mtmt) cc_final: 0.7135 (mmtt) REVERT: A 820 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7249 (mm) REVERT: A 848 SER cc_start: 0.6508 (OUTLIER) cc_final: 0.6274 (p) REVERT: A 1201 MET cc_start: 0.7087 (tpp) cc_final: 0.6882 (tpp) REVERT: A 1309 VAL cc_start: 0.7554 (p) cc_final: 0.7343 (m) REVERT: A 1349 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6686 (pt0) REVERT: A 1435 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7140 (pt) REVERT: A 1436 TYR cc_start: 0.7786 (t80) cc_final: 0.7484 (t80) REVERT: A 1465 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8081 (pptt) REVERT: A 1528 ASN cc_start: 0.7756 (t0) cc_final: 0.7454 (t0) REVERT: A 1532 MET cc_start: 0.8737 (mtt) cc_final: 0.8365 (mtt) REVERT: A 1537 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: A 1541 GLN cc_start: 0.8372 (tp40) cc_final: 0.8091 (tp40) REVERT: A 1543 MET cc_start: 0.7112 (ttp) cc_final: 0.6714 (tpt) REVERT: A 1732 ASN cc_start: 0.7410 (t0) cc_final: 0.7095 (t0) REVERT: B 99 LYS cc_start: 0.7055 (tptm) cc_final: 0.6753 (tppt) REVERT: B 160 GLU cc_start: 0.7331 (tt0) cc_final: 0.7059 (tt0) REVERT: B 162 MET cc_start: 0.6182 (tpt) cc_final: 0.5888 (tpt) REVERT: B 166 LEU cc_start: 0.8293 (mt) cc_final: 0.8093 (mt) REVERT: B 182 TYR cc_start: 0.8083 (t80) cc_final: 0.7877 (t80) REVERT: F 85 MET cc_start: 0.2249 (mmm) cc_final: 0.1751 (mmm) outliers start: 57 outliers final: 31 residues processed: 309 average time/residue: 0.0845 time to fit residues: 38.2617 Evaluate side-chains 250 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 146 ASN A 240 GLN A 365 ASN A 395 ASN A 410 GLN A 766 HIS A 941 GLN ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1276 ASN A1341 ASN A1502 ASN A1514 ASN ** A1528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 ASN A1709 ASN B 102 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.225681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.180734 restraints weight = 12560.605| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.75 r_work: 0.3681 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11983 Z= 0.154 Angle : 0.704 14.794 16259 Z= 0.355 Chirality : 0.044 0.301 1886 Planarity : 0.004 0.052 1978 Dihedral : 8.174 99.813 1626 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.05 % Allowed : 23.46 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.21), residues: 1419 helix: -0.29 (0.17), residues: 861 sheet: -0.85 (0.49), residues: 117 loop : -2.24 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 94 TYR 0.024 0.002 TYR A1739 PHE 0.020 0.001 PHE A 165 TRP 0.021 0.001 TRP A 151 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11965) covalent geometry : angle 0.69257 / 0.35 (16214) SS BOND : bond 0.00722 / 0.36 ( 9) SS BOND : angle 1.95529 / 1.32 ( 18) hydrogen bonds : bond 0.04708 / 3.10 ( 746) hydrogen bonds : angle 4.90237 / 3.49 ( 2145) link_BETA1-4 : bond 0.00533 / 0.38 ( 2) link_BETA1-4 : angle 3.60862 / 1.98 ( 6) link_NAG-ASN : bond 0.00591 / 0.28 ( 7) link_NAG-ASN : angle 2.47379 / 1.46 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 300 ARG cc_start: 0.7333 (ttm-80) cc_final: 0.7004 (mtt-85) REVERT: A 301 LYS cc_start: 0.7704 (mtmt) cc_final: 0.7329 (mmtt) REVERT: A 742 MET cc_start: 0.5164 (mmm) cc_final: 0.3417 (mtp) REVERT: A 820 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7469 (mm) REVERT: A 1236 ILE cc_start: 0.8583 (mt) cc_final: 0.8379 (mp) REVERT: A 1287 LYS cc_start: 0.8469 (tptp) cc_final: 0.8262 (tppt) REVERT: A 1305 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: A 1309 VAL cc_start: 0.8076 (p) cc_final: 0.7806 (m) REVERT: A 1349 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7039 (pm20) REVERT: A 1435 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7394 (pt) REVERT: A 1464 LYS cc_start: 0.7694 (tttm) cc_final: 0.7456 (ttmm) REVERT: A 1465 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8123 (pptt) REVERT: A 1466 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8059 (mtpt) REVERT: A 1518 ASP cc_start: 0.8177 (m-30) cc_final: 0.7761 (m-30) REVERT: A 1541 GLN cc_start: 0.8390 (tp40) cc_final: 0.8167 (tp40) REVERT: A 1565 LYS cc_start: 0.8737 (pttm) cc_final: 0.8305 (ptpp) REVERT: A 1658 TYR cc_start: 0.8225 (m-80) cc_final: 0.7954 (m-80) REVERT: A 1714 ASP cc_start: 0.6529 (m-30) cc_final: 0.6244 (m-30) REVERT: A 1732 ASN cc_start: 0.7513 (t0) cc_final: 0.7263 (t0) REVERT: B 34 MET cc_start: 0.6299 (mmm) cc_final: 0.6062 (mmt) REVERT: B 69 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8040 (ttpt) REVERT: B 99 LYS cc_start: 0.7248 (tptm) cc_final: 0.6988 (tppt) REVERT: B 162 MET cc_start: 0.6640 (tpt) cc_final: 0.6380 (tpt) REVERT: B 182 TYR cc_start: 0.7866 (t80) cc_final: 0.7401 (t80) outliers start: 39 outliers final: 20 residues processed: 262 average time/residue: 0.0909 time to fit residues: 34.7057 Evaluate side-chains 240 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 138 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 141 optimal weight: 50.0000 chunk 112 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A 780 ASN A 961 ASN A1276 ASN ** A1528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 ASN A1665 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.224104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.180958 restraints weight = 12591.134| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.84 r_work: 0.3643 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11983 Z= 0.177 Angle : 0.684 15.635 16259 Z= 0.344 Chirality : 0.044 0.290 1886 Planarity : 0.004 0.042 1978 Dihedral : 6.451 57.158 1579 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.53 % Allowed : 23.06 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.21), residues: 1419 helix: 0.04 (0.17), residues: 866 sheet: -0.95 (0.46), residues: 120 loop : -2.12 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1290 TYR 0.020 0.002 TYR A1739 PHE 0.017 0.001 PHE A1197 TRP 0.014 0.001 TRP A 151 HIS 0.003 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (11965) covalent geometry : angle 0.67352 / 0.34 (16214) SS BOND : bond 0.00518 / 0.29 ( 9) SS BOND : angle 1.34800 / 0.76 ( 18) hydrogen bonds : bond 0.04585 / 3.00 ( 746) hydrogen bonds : angle 4.91698 / 3.49 ( 2145) link_BETA1-4 : bond 0.00382 / 0.27 ( 2) link_BETA1-4 : angle 3.57774 / 1.94 ( 6) link_NAG-ASN : bond 0.00344 / 0.16 ( 7) link_NAG-ASN : angle 2.68113 / 1.58 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.7024 (pt) cc_final: 0.6771 (mt) REVERT: A 300 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7136 (mtt-85) REVERT: A 301 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7268 (mmtt) REVERT: A 798 MET cc_start: 0.4169 (ptm) cc_final: 0.3905 (ptp) REVERT: A 820 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7576 (mm) REVERT: A 1236 ILE cc_start: 0.8538 (mt) cc_final: 0.8329 (mp) REVERT: A 1287 LYS cc_start: 0.8500 (tptp) cc_final: 0.8293 (tppt) REVERT: A 1305 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: A 1309 VAL cc_start: 0.8124 (p) cc_final: 0.7838 (m) REVERT: A 1349 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7085 (pm20) REVERT: A 1435 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7390 (pt) REVERT: A 1464 LYS cc_start: 0.7717 (tttm) cc_final: 0.7498 (ttmm) REVERT: A 1465 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8107 (pptt) REVERT: A 1466 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8089 (mtpt) REVERT: A 1518 ASP cc_start: 0.8274 (m-30) cc_final: 0.7838 (m-30) REVERT: A 1541 GLN cc_start: 0.8291 (tp40) cc_final: 0.8089 (tp40) REVERT: A 1565 LYS cc_start: 0.8795 (pttm) cc_final: 0.8502 (pttt) REVERT: A 1610 ARG cc_start: 0.6041 (mtp85) cc_final: 0.5698 (mtp180) REVERT: A 1727 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: B 69 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8023 (ttpt) REVERT: B 99 LYS cc_start: 0.7293 (tptm) cc_final: 0.6961 (tppt) REVERT: B 154 MET cc_start: 0.6801 (mtt) cc_final: 0.6302 (mtm) REVERT: B 162 MET cc_start: 0.6686 (tpt) cc_final: 0.6424 (tpt) REVERT: B 182 TYR cc_start: 0.7861 (t80) cc_final: 0.7352 (t80) outliers start: 58 outliers final: 27 residues processed: 261 average time/residue: 0.0861 time to fit residues: 32.9209 Evaluate side-chains 243 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1390 ASP Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 138 optimal weight: 30.0000 chunk 67 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN A 265 GLN A 395 ASN A1276 ASN A1528 ASN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.227116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.179165 restraints weight = 12625.211| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 3.59 r_work: 0.3684 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11983 Z= 0.134 Angle : 0.633 11.858 16259 Z= 0.320 Chirality : 0.042 0.294 1886 Planarity : 0.004 0.039 1978 Dihedral : 6.225 58.248 1577 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 4.38 % Allowed : 22.67 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1419 helix: 0.40 (0.17), residues: 862 sheet: -0.79 (0.46), residues: 117 loop : -1.97 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.019 0.001 TYR A1739 PHE 0.021 0.001 PHE A1197 TRP 0.017 0.001 TRP A 151 HIS 0.003 0.000 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (11965) covalent geometry : angle 0.62150 / 0.32 (16214) SS BOND : bond 0.00384 / 0.24 ( 9) SS BOND : angle 0.89693 / 0.48 ( 18) hydrogen bonds : bond 0.04254 / 2.75 ( 746) hydrogen bonds : angle 4.77523 / 3.40 ( 2145) link_BETA1-4 : bond 0.00622 / 0.44 ( 2) link_BETA1-4 : angle 3.52571 / 1.92 ( 6) link_NAG-ASN : bond 0.00386 / 0.18 ( 7) link_NAG-ASN : angle 2.71716 / 1.59 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.8667 (t) cc_final: 0.8275 (p) REVERT: A 222 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8090 (mt) REVERT: A 300 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.6980 (mtt-85) REVERT: A 301 LYS cc_start: 0.7617 (mtmt) cc_final: 0.7173 (mmtt) REVERT: A 742 MET cc_start: 0.3728 (mmt) cc_final: 0.2481 (mtp) REVERT: A 798 MET cc_start: 0.4411 (ptm) cc_final: 0.4191 (ptm) REVERT: A 1201 MET cc_start: 0.7993 (tpp) cc_final: 0.7760 (mmt) REVERT: A 1254 PHE cc_start: 0.7451 (m-10) cc_final: 0.7197 (m-80) REVERT: A 1305 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: A 1309 VAL cc_start: 0.8041 (p) cc_final: 0.7792 (m) REVERT: A 1349 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6806 (pt0) REVERT: A 1435 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7327 (pt) REVERT: A 1465 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8077 (pptt) REVERT: A 1466 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8160 (mtpt) REVERT: A 1518 ASP cc_start: 0.8249 (m-30) cc_final: 0.7803 (m-30) REVERT: A 1541 GLN cc_start: 0.8334 (tp40) cc_final: 0.7822 (tp40) REVERT: A 1610 ARG cc_start: 0.6173 (mtp85) cc_final: 0.5893 (mtp180) REVERT: A 1658 TYR cc_start: 0.8241 (m-80) cc_final: 0.7923 (m-80) REVERT: A 1727 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: B 69 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8108 (ttpt) REVERT: B 74 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: B 99 LYS cc_start: 0.7148 (tptm) cc_final: 0.6794 (tppt) REVERT: B 154 MET cc_start: 0.6757 (mtt) cc_final: 0.6295 (mtm) REVERT: B 162 MET cc_start: 0.6609 (tpt) cc_final: 0.6356 (tpt) REVERT: B 182 TYR cc_start: 0.7867 (t80) cc_final: 0.7400 (t80) outliers start: 56 outliers final: 29 residues processed: 269 average time/residue: 0.0902 time to fit residues: 35.3549 Evaluate side-chains 253 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 911 ASN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.227193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.180835 restraints weight = 12483.691| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.70 r_work: 0.3682 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11983 Z= 0.134 Angle : 0.630 11.187 16259 Z= 0.320 Chirality : 0.042 0.294 1886 Planarity : 0.004 0.038 1978 Dihedral : 5.882 58.521 1575 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 4.85 % Allowed : 24.08 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1419 helix: 0.57 (0.17), residues: 860 sheet: -0.73 (0.45), residues: 126 loop : -1.80 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1290 TYR 0.024 0.002 TYR A1482 PHE 0.010 0.001 PHE A 913 TRP 0.018 0.001 TRP A 151 HIS 0.003 0.000 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (11965) covalent geometry : angle 0.62224 / 0.32 (16214) SS BOND : bond 0.00431 / 0.28 ( 9) SS BOND : angle 0.93997 / 0.62 ( 18) hydrogen bonds : bond 0.04186 / 2.72 ( 746) hydrogen bonds : angle 4.74289 / 3.39 ( 2145) link_BETA1-4 : bond 0.00727 / 0.52 ( 2) link_BETA1-4 : angle 3.43902 / 1.88 ( 6) link_NAG-ASN : bond 0.00363 / 0.17 ( 7) link_NAG-ASN : angle 1.98422 / 1.08 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 227 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.8678 (t) cc_final: 0.8300 (p) REVERT: A 222 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8026 (mt) REVERT: A 300 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.6949 (mtt-85) REVERT: A 301 LYS cc_start: 0.7576 (mtmt) cc_final: 0.7135 (mmtt) REVERT: A 742 MET cc_start: 0.3671 (mmt) cc_final: 0.2461 (mtp) REVERT: A 768 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.6027 (ttm) REVERT: A 798 MET cc_start: 0.4287 (ptm) cc_final: 0.3948 (ptm) REVERT: A 820 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7223 (mm) REVERT: A 1201 MET cc_start: 0.8083 (tpp) cc_final: 0.7656 (tpp) REVERT: A 1254 PHE cc_start: 0.7383 (m-10) cc_final: 0.7025 (m-80) REVERT: A 1287 LYS cc_start: 0.8308 (tppt) cc_final: 0.7738 (mttm) REVERT: A 1305 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: A 1309 VAL cc_start: 0.8043 (p) cc_final: 0.7822 (m) REVERT: A 1349 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6808 (pt0) REVERT: A 1435 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7299 (pt) REVERT: A 1436 TYR cc_start: 0.7876 (t80) cc_final: 0.7602 (t80) REVERT: A 1447 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7374 (t80) REVERT: A 1540 SER cc_start: 0.7537 (t) cc_final: 0.7319 (m) REVERT: A 1541 GLN cc_start: 0.8300 (tp40) cc_final: 0.7605 (tp40) REVERT: A 1658 TYR cc_start: 0.8188 (m-80) cc_final: 0.7837 (m-80) REVERT: A 1727 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: B 69 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8127 (ttpt) REVERT: B 87 GLU cc_start: 0.7555 (tt0) cc_final: 0.7315 (mt-10) REVERT: B 99 LYS cc_start: 0.7043 (tptm) cc_final: 0.6792 (tppt) REVERT: B 152 ARG cc_start: 0.8011 (ptm160) cc_final: 0.6770 (ptm-80) REVERT: B 154 MET cc_start: 0.6673 (mtt) cc_final: 0.6268 (mtm) REVERT: B 160 GLU cc_start: 0.7513 (tt0) cc_final: 0.7213 (tt0) REVERT: B 162 MET cc_start: 0.6577 (tpt) cc_final: 0.6311 (tpt) REVERT: B 182 TYR cc_start: 0.7784 (t80) cc_final: 0.7392 (t80) outliers start: 62 outliers final: 35 residues processed: 270 average time/residue: 0.0915 time to fit residues: 36.2657 Evaluate side-chains 255 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1447 PHE Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1672 GLU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.227603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.179854 restraints weight = 12528.972| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.41 r_work: 0.3723 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11983 Z= 0.130 Angle : 0.625 10.837 16259 Z= 0.317 Chirality : 0.042 0.294 1886 Planarity : 0.004 0.041 1978 Dihedral : 5.721 59.366 1575 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.22 % Allowed : 24.71 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1419 helix: 0.66 (0.17), residues: 862 sheet: -0.61 (0.46), residues: 126 loop : -1.73 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.031 0.001 TYR A1482 PHE 0.023 0.001 PHE A1197 TRP 0.019 0.001 TRP A 151 HIS 0.003 0.000 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (11965) covalent geometry : angle 0.61437 / 0.31 (16214) SS BOND : bond 0.00355 / 0.23 ( 9) SS BOND : angle 0.81449 / 0.49 ( 18) hydrogen bonds : bond 0.04129 / 2.69 ( 746) hydrogen bonds : angle 4.72880 / 3.39 ( 2145) link_BETA1-4 : bond 0.00672 / 0.48 ( 2) link_BETA1-4 : angle 3.43621 / 1.88 ( 6) link_NAG-ASN : bond 0.00401 / 0.19 ( 7) link_NAG-ASN : angle 2.72388 / 1.70 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8572 (mp) REVERT: A 146 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7518 (t0) REVERT: A 164 THR cc_start: 0.8663 (t) cc_final: 0.8348 (p) REVERT: A 222 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8026 (mt) REVERT: A 301 LYS cc_start: 0.7528 (mtmt) cc_final: 0.7134 (mmtt) REVERT: A 742 MET cc_start: 0.3647 (mmt) cc_final: 0.2497 (mtt) REVERT: A 798 MET cc_start: 0.4230 (ptm) cc_final: 0.3869 (ptm) REVERT: A 1201 MET cc_start: 0.8040 (tpp) cc_final: 0.7770 (mmt) REVERT: A 1254 PHE cc_start: 0.7240 (m-10) cc_final: 0.6892 (m-80) REVERT: A 1287 LYS cc_start: 0.8259 (tppt) cc_final: 0.7681 (mtpp) REVERT: A 1305 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: A 1349 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.6857 (pt0) REVERT: A 1435 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7269 (pt) REVERT: A 1436 TYR cc_start: 0.7885 (t80) cc_final: 0.7634 (t80) REVERT: A 1540 SER cc_start: 0.7528 (t) cc_final: 0.7308 (m) REVERT: A 1541 GLN cc_start: 0.8335 (tp40) cc_final: 0.7640 (tp40) REVERT: A 1565 LYS cc_start: 0.8593 (pttm) cc_final: 0.8192 (ptpt) REVERT: A 1665 ASN cc_start: 0.8056 (m110) cc_final: 0.6266 (m-40) REVERT: A 1727 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: B 69 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8218 (ttpt) REVERT: B 74 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: B 87 GLU cc_start: 0.7551 (tt0) cc_final: 0.7319 (mt-10) REVERT: B 154 MET cc_start: 0.6661 (mtt) cc_final: 0.6289 (mtm) REVERT: B 160 GLU cc_start: 0.7448 (tt0) cc_final: 0.7113 (tt0) REVERT: B 162 MET cc_start: 0.6584 (tpt) cc_final: 0.6324 (tpt) REVERT: B 182 TYR cc_start: 0.7792 (t80) cc_final: 0.7438 (t80) outliers start: 54 outliers final: 27 residues processed: 259 average time/residue: 0.0931 time to fit residues: 35.3306 Evaluate side-chains 247 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 963 PHE Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 141 optimal weight: 40.0000 chunk 120 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A1579 ASN B 102 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.221968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.173988 restraints weight = 12553.231| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.28 r_work: 0.3597 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11983 Z= 0.218 Angle : 0.712 12.905 16259 Z= 0.359 Chirality : 0.045 0.289 1886 Planarity : 0.004 0.043 1978 Dihedral : 5.810 59.830 1573 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.91 % Allowed : 25.33 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1419 helix: 0.52 (0.17), residues: 860 sheet: -0.55 (0.46), residues: 126 loop : -1.73 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1290 TYR 0.037 0.002 TYR A1482 PHE 0.023 0.002 PHE A1740 TRP 0.020 0.001 TRP A 151 HIS 0.004 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 (11965) covalent geometry : angle 0.70339 / 0.36 (16214) SS BOND : bond 0.00617 / 0.37 ( 9) SS BOND : angle 1.39186 / 0.82 ( 18) hydrogen bonds : bond 0.04483 / 2.92 ( 746) hydrogen bonds : angle 4.93475 / 3.54 ( 2145) link_BETA1-4 : bond 0.00727 / 0.52 ( 2) link_BETA1-4 : angle 3.32126 / 1.85 ( 6) link_NAG-ASN : bond 0.00382 / 0.20 ( 7) link_NAG-ASN : angle 2.46155 / 1.38 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 164 THR cc_start: 0.8661 (t) cc_final: 0.8336 (p) REVERT: A 301 LYS cc_start: 0.7712 (mtmt) cc_final: 0.7297 (mmtt) REVERT: A 742 MET cc_start: 0.3676 (mmt) cc_final: 0.2534 (mtt) REVERT: A 768 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5945 (ttm) REVERT: A 798 MET cc_start: 0.4019 (ptm) cc_final: 0.3657 (ptm) REVERT: A 946 ILE cc_start: 0.8602 (mt) cc_final: 0.8310 (mp) REVERT: A 1201 MET cc_start: 0.8162 (tpp) cc_final: 0.7908 (mmt) REVERT: A 1254 PHE cc_start: 0.7425 (m-10) cc_final: 0.6913 (m-80) REVERT: A 1287 LYS cc_start: 0.8308 (tppt) cc_final: 0.7700 (mtpp) REVERT: A 1305 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: A 1309 VAL cc_start: 0.7964 (p) cc_final: 0.7646 (m) REVERT: A 1349 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.6969 (pt0) REVERT: A 1435 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7337 (pt) REVERT: A 1447 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7398 (t80) REVERT: A 1665 ASN cc_start: 0.8181 (m110) cc_final: 0.7298 (m-40) REVERT: A 1727 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: B 152 ARG cc_start: 0.7976 (ptm-80) cc_final: 0.7662 (ptt90) REVERT: B 154 MET cc_start: 0.6624 (mtt) cc_final: 0.6260 (mtm) REVERT: B 160 GLU cc_start: 0.7474 (tt0) cc_final: 0.7107 (tt0) REVERT: B 162 MET cc_start: 0.6519 (tpt) cc_final: 0.6259 (tpt) REVERT: B 182 TYR cc_start: 0.7789 (t80) cc_final: 0.7452 (t80) outliers start: 50 outliers final: 33 residues processed: 251 average time/residue: 0.0975 time to fit residues: 36.2260 Evaluate side-chains 251 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1447 PHE Chi-restraints excluded: chain A residue 1482 TYR Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 83 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A1541 GLN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.225850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.180247 restraints weight = 12456.748| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.44 r_work: 0.3717 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11983 Z= 0.134 Angle : 0.641 11.003 16259 Z= 0.324 Chirality : 0.042 0.293 1886 Planarity : 0.004 0.042 1978 Dihedral : 5.498 59.347 1569 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.36 % Allowed : 25.72 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.22), residues: 1419 helix: 0.69 (0.17), residues: 862 sheet: -0.42 (0.46), residues: 126 loop : -1.66 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 214 TYR 0.045 0.002 TYR A1739 PHE 0.033 0.001 PHE A1666 TRP 0.026 0.001 TRP A 151 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11965) covalent geometry : angle 0.63408 / 0.32 (16214) SS BOND : bond 0.00368 / 0.24 ( 9) SS BOND : angle 0.84493 / 0.50 ( 18) hydrogen bonds : bond 0.04097 / 2.67 ( 746) hydrogen bonds : angle 4.77270 / 3.42 ( 2145) link_BETA1-4 : bond 0.00649 / 0.46 ( 2) link_BETA1-4 : angle 3.42289 / 1.88 ( 6) link_NAG-ASN : bond 0.00275 / 0.12 ( 7) link_NAG-ASN : angle 1.85447 / 1.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 164 THR cc_start: 0.8677 (t) cc_final: 0.8386 (p) REVERT: A 301 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7037 (mmtt) REVERT: A 742 MET cc_start: 0.3752 (mmt) cc_final: 0.2570 (mtt) REVERT: A 768 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.6109 (ttm) REVERT: A 798 MET cc_start: 0.4184 (ptm) cc_final: 0.3749 (ptm) REVERT: A 946 ILE cc_start: 0.8567 (mt) cc_final: 0.8259 (mp) REVERT: A 1201 MET cc_start: 0.8191 (tpp) cc_final: 0.7940 (mmt) REVERT: A 1254 PHE cc_start: 0.7400 (m-10) cc_final: 0.7019 (m-80) REVERT: A 1287 LYS cc_start: 0.8325 (tppt) cc_final: 0.7725 (mttp) REVERT: A 1305 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: A 1309 VAL cc_start: 0.8025 (p) cc_final: 0.7744 (m) REVERT: A 1349 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7026 (pt0) REVERT: A 1435 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7429 (pt) REVERT: A 1541 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7896 (tp-100) REVERT: A 1665 ASN cc_start: 0.8264 (m110) cc_final: 0.7165 (m110) REVERT: A 1714 ASP cc_start: 0.6687 (m-30) cc_final: 0.6448 (m-30) REVERT: A 1727 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: B 69 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8212 (ttpt) REVERT: B 83 ASP cc_start: 0.7947 (t0) cc_final: 0.7550 (t0) REVERT: B 87 GLU cc_start: 0.7672 (tt0) cc_final: 0.7418 (mt-10) REVERT: B 152 ARG cc_start: 0.7858 (ptm-80) cc_final: 0.7535 (ptt90) REVERT: B 154 MET cc_start: 0.6601 (mtt) cc_final: 0.6173 (mtm) REVERT: B 160 GLU cc_start: 0.7402 (tt0) cc_final: 0.7029 (tt0) REVERT: B 162 MET cc_start: 0.6611 (tpt) cc_final: 0.6354 (tpt) REVERT: B 182 TYR cc_start: 0.7686 (t80) cc_final: 0.7345 (t80) outliers start: 43 outliers final: 31 residues processed: 238 average time/residue: 0.0946 time to fit residues: 32.8871 Evaluate side-chains 245 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 963 PHE Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1672 GLU Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 140 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A 395 ASN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.225455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.177884 restraints weight = 12308.556| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.77 r_work: 0.3674 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11983 Z= 0.144 Angle : 0.651 11.195 16259 Z= 0.328 Chirality : 0.043 0.290 1886 Planarity : 0.004 0.040 1978 Dihedral : 5.391 57.200 1567 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.05 % Allowed : 26.19 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1419 helix: 0.73 (0.17), residues: 862 sheet: -0.35 (0.47), residues: 126 loop : -1.61 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1290 TYR 0.035 0.002 TYR A1739 PHE 0.024 0.001 PHE A1666 TRP 0.027 0.001 TRP A 151 HIS 0.001 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11965) covalent geometry : angle 0.63969 / 0.33 (16214) SS BOND : bond 0.00441 / 0.27 ( 9) SS BOND : angle 1.17265 / 0.62 ( 18) hydrogen bonds : bond 0.04087 / 2.66 ( 746) hydrogen bonds : angle 4.76932 / 3.43 ( 2145) link_BETA1-4 : bond 0.00767 / 0.55 ( 2) link_BETA1-4 : angle 3.28829 / 1.82 ( 6) link_NAG-ASN : bond 0.00235 / 0.11 ( 7) link_NAG-ASN : angle 2.72264 / 1.58 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8529 (mp) REVERT: A 164 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8398 (p) REVERT: A 301 LYS cc_start: 0.7574 (mtmt) cc_final: 0.7129 (mmtt) REVERT: A 742 MET cc_start: 0.3693 (mmt) cc_final: 0.2484 (mtp) REVERT: A 768 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5946 (ttm) REVERT: A 798 MET cc_start: 0.3963 (ptm) cc_final: 0.3595 (ptm) REVERT: A 946 ILE cc_start: 0.8575 (mt) cc_final: 0.8252 (mp) REVERT: A 1201 MET cc_start: 0.8029 (tpp) cc_final: 0.7805 (mmt) REVERT: A 1254 PHE cc_start: 0.7228 (m-10) cc_final: 0.6856 (m-80) REVERT: A 1287 LYS cc_start: 0.8298 (tppt) cc_final: 0.7760 (mttp) REVERT: A 1305 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7014 (tt0) REVERT: A 1309 VAL cc_start: 0.7916 (p) cc_final: 0.7680 (m) REVERT: A 1349 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: A 1435 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7292 (pt) REVERT: A 1540 SER cc_start: 0.7546 (t) cc_final: 0.7301 (m) REVERT: A 1541 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7753 (tp-100) REVERT: A 1565 LYS cc_start: 0.8767 (pttm) cc_final: 0.8142 (ptpt) REVERT: A 1665 ASN cc_start: 0.8190 (m110) cc_final: 0.6427 (m-40) REVERT: A 1727 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: B 69 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8246 (ttpt) REVERT: B 72 ARG cc_start: 0.7112 (ttp80) cc_final: 0.6338 (ttt-90) REVERT: B 83 ASP cc_start: 0.7928 (t0) cc_final: 0.7617 (t0) REVERT: B 87 GLU cc_start: 0.7572 (tt0) cc_final: 0.7326 (mt-10) REVERT: B 160 GLU cc_start: 0.7386 (tt0) cc_final: 0.7017 (tt0) REVERT: B 162 MET cc_start: 0.6559 (tpt) cc_final: 0.6301 (tpt) REVERT: B 182 TYR cc_start: 0.7689 (t80) cc_final: 0.7429 (t80) outliers start: 39 outliers final: 28 residues processed: 234 average time/residue: 0.1025 time to fit residues: 34.7999 Evaluate side-chains 244 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 963 PHE Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1701 ASP Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 13 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 94 optimal weight: 0.0980 chunk 6 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A 395 ASN A1551 ASN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.226727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.181000 restraints weight = 12457.959| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.70 r_work: 0.3702 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11983 Z= 0.135 Angle : 0.655 12.909 16259 Z= 0.331 Chirality : 0.042 0.289 1886 Planarity : 0.004 0.040 1978 Dihedral : 5.394 55.972 1565 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.28 % Allowed : 25.96 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.22), residues: 1419 helix: 0.78 (0.17), residues: 863 sheet: -0.30 (0.46), residues: 126 loop : -1.63 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 152 TYR 0.049 0.001 TYR A1739 PHE 0.015 0.001 PHE A1740 TRP 0.029 0.001 TRP A 151 HIS 0.001 0.000 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (11965) covalent geometry : angle 0.64442 / 0.33 (16214) SS BOND : bond 0.00739 / 0.37 ( 9) SS BOND : angle 1.99786 / 0.68 ( 18) hydrogen bonds : bond 0.04005 / 2.62 ( 746) hydrogen bonds : angle 4.72485 / 3.40 ( 2145) link_BETA1-4 : bond 0.00721 / 0.51 ( 2) link_BETA1-4 : angle 3.29817 / 1.82 ( 6) link_NAG-ASN : bond 0.00258 / 0.11 ( 7) link_NAG-ASN : angle 2.28728 / 1.23 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 164 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8379 (p) REVERT: A 214 ARG cc_start: 0.6413 (ttt90) cc_final: 0.6203 (ttt-90) REVERT: A 301 LYS cc_start: 0.7540 (mtmt) cc_final: 0.7138 (mmtt) REVERT: A 742 MET cc_start: 0.3720 (mmt) cc_final: 0.2552 (mtp) REVERT: A 768 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.6010 (ttm) REVERT: A 798 MET cc_start: 0.4083 (ptm) cc_final: 0.3707 (ptm) REVERT: A 946 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 1201 MET cc_start: 0.8060 (tpp) cc_final: 0.7829 (mmt) REVERT: A 1254 PHE cc_start: 0.7113 (m-10) cc_final: 0.6733 (m-80) REVERT: A 1287 LYS cc_start: 0.8215 (tppt) cc_final: 0.7677 (mttp) REVERT: A 1305 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: A 1349 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.6575 (pm20) REVERT: A 1435 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7294 (pt) REVERT: A 1540 SER cc_start: 0.7655 (t) cc_final: 0.7417 (m) REVERT: A 1541 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7767 (tp-100) REVERT: A 1565 LYS cc_start: 0.8720 (pttm) cc_final: 0.8161 (ptpt) REVERT: A 1665 ASN cc_start: 0.8110 (m110) cc_final: 0.6378 (m-40) REVERT: A 1727 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: B 69 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8259 (ttpt) REVERT: B 83 ASP cc_start: 0.7971 (t0) cc_final: 0.7667 (t0) REVERT: B 87 GLU cc_start: 0.7517 (tt0) cc_final: 0.7270 (mt-10) REVERT: B 160 GLU cc_start: 0.7345 (tt0) cc_final: 0.6954 (tt0) REVERT: B 162 MET cc_start: 0.6614 (tpt) cc_final: 0.6373 (tpt) REVERT: B 182 TYR cc_start: 0.7672 (t80) cc_final: 0.7420 (t80) outliers start: 42 outliers final: 29 residues processed: 235 average time/residue: 0.0953 time to fit residues: 33.2501 Evaluate side-chains 242 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 963 PHE Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1701 ASP Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 126 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A 395 ASN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.224057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177966 restraints weight = 12436.950| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.67 r_work: 0.3681 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11983 Z= 0.165 Angle : 0.685 12.357 16259 Z= 0.344 Chirality : 0.044 0.284 1886 Planarity : 0.004 0.038 1978 Dihedral : 5.393 53.417 1565 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.28 % Allowed : 26.51 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1419 helix: 0.75 (0.17), residues: 862 sheet: -0.33 (0.47), residues: 126 loop : -1.67 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 217 TYR 0.048 0.002 TYR A1739 PHE 0.019 0.001 PHE A1740 TRP 0.023 0.001 TRP A 151 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11965) covalent geometry : angle 0.67192 / 0.34 (16214) SS BOND : bond 0.00812 / 0.42 ( 9) SS BOND : angle 2.03271 / 0.73 ( 18) hydrogen bonds : bond 0.04167 / 2.71 ( 746) hydrogen bonds : angle 4.82727 / 3.48 ( 2145) link_BETA1-4 : bond 0.00763 / 0.55 ( 2) link_BETA1-4 : angle 3.17557 / 1.77 ( 6) link_NAG-ASN : bond 0.00335 / 0.16 ( 7) link_NAG-ASN : angle 2.82164 / 1.42 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.49 seconds wall clock time: 51 minutes 51.80 seconds (3111.80 seconds total)