Starting phenix.real_space_refine on Wed Mar 4 09:33:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xmg_33296/03_2026/7xmg_33296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmg_33296/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xmg_33296/03_2026/7xmg_33296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmg_33296/03_2026/7xmg_33296.map" model { file = "/net/cci-nas-00/data/ceres_data/7xmg_33296/03_2026/7xmg_33296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmg_33296/03_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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.83, per 1000 atoms: 0.24 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: 1.02 Conformation dependent library (CDL) restraints added in 409.6 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: 0.33 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: 1.93 Time building geometry restraints manager: 1.27 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 - 24.60: 6608 24.60 - 49.21: 485 49.21 - 73.81: 61 73.81 - 98.42: 17 98.42 - 123.02: 3 Dihedral angle restraints: 7174 sinusoidal: 2980 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 7171 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 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 : 16.614 123.021 4437 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 covalent geometry : bond 0.00607 (11965) covalent geometry : angle 0.84721 (16214) SS BOND : bond 0.29796 ( 9) SS BOND : angle 19.29465 ( 18) hydrogen bonds : bond 0.10118 ( 746) hydrogen bonds : angle 4.82408 ( 2145) link_BETA1-4 : bond 0.00162 ( 2) link_BETA1-4 : angle 4.50437 ( 6) link_NAG-ASN : bond 0.00509 ( 7) link_NAG-ASN : angle 2.55441 ( 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 : 0.349 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: 0.0990 time to fit residues: 44.7998 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 : 0.285 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.225731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.178714 restraints weight = 12560.976| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.75 r_work: 0.3664 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1416 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= 0.154 Angle : 0.708 14.653 16259 Z= 0.356 Chirality : 0.044 0.286 1886 Planarity : 0.004 0.052 1978 Dihedral : 9.431 107.553 1815 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.05 % Allowed : 23.53 % Favored : 73.42 % 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: -1.47 (0.21), residues: 1419 helix: -0.28 (0.17), residues: 861 sheet: -0.84 (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 0.025 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 covalent geometry : bond 0.00330 (11965) covalent geometry : angle 0.69592 (16214) SS BOND : bond 0.00764 ( 9) SS BOND : angle 1.96475 ( 18) hydrogen bonds : bond 0.04704 ( 746) hydrogen bonds : angle 4.90354 ( 2145) link_BETA1-4 : bond 0.00308 ( 2) link_BETA1-4 : angle 4.12038 ( 6) link_NAG-ASN : bond 0.00569 ( 7) link_NAG-ASN : angle 2.50459 ( 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 274 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 300 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.6921 (mtt-85) REVERT: A 301 LYS cc_start: 0.7681 (mtmt) cc_final: 0.7202 (mmtt) REVERT: A 742 MET cc_start: 0.5059 (mmm) cc_final: 0.3423 (mtp) REVERT: A 820 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7481 (mm) REVERT: A 1236 ILE cc_start: 0.8533 (mt) cc_final: 0.8305 (mp) REVERT: A 1287 LYS cc_start: 0.8467 (tptp) cc_final: 0.8265 (tppt) REVERT: A 1305 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: A 1309 VAL cc_start: 0.7950 (p) cc_final: 0.7672 (m) REVERT: A 1349 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: A 1435 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7399 (pt) REVERT: A 1464 LYS cc_start: 0.7678 (tttm) cc_final: 0.7411 (ttmm) REVERT: A 1465 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8108 (pptt) REVERT: A 1466 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8068 (mtpt) REVERT: A 1518 ASP cc_start: 0.8224 (m-30) cc_final: 0.7790 (m-30) REVERT: A 1541 GLN cc_start: 0.8433 (tp40) cc_final: 0.8193 (tp40) REVERT: A 1565 LYS cc_start: 0.8735 (pttm) cc_final: 0.8321 (ptpp) REVERT: A 1658 TYR cc_start: 0.8311 (m-80) cc_final: 0.8051 (m-80) REVERT: A 1714 ASP cc_start: 0.6455 (m-30) cc_final: 0.6216 (m-30) REVERT: A 1732 ASN cc_start: 0.7540 (t0) cc_final: 0.7294 (t0) REVERT: B 34 MET cc_start: 0.6301 (mmm) cc_final: 0.6053 (mmt) REVERT: B 69 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7995 (ttpt) REVERT: B 99 LYS cc_start: 0.7239 (tptm) cc_final: 0.6876 (tppt) REVERT: B 162 MET cc_start: 0.6529 (tpt) cc_final: 0.6292 (tpt) REVERT: B 182 TYR cc_start: 0.7817 (t80) cc_final: 0.7369 (t80) outliers start: 39 outliers final: 20 residues processed: 264 average time/residue: 0.1020 time to fit residues: 38.8973 Evaluate side-chains 241 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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: 7.9990 chunk 18 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 139 optimal weight: 30.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN A 961 ASN A1276 ASN ** A1528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 ASN A1665 ASN B 102 GLN ** 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 = 0.4507 r_free = 0.4507 target = 0.220790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.163655 restraints weight = 12606.618| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.11 r_work: 0.3654 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11983 Z= 0.245 Angle : 0.751 17.126 16259 Z= 0.376 Chirality : 0.047 0.303 1886 Planarity : 0.004 0.044 1978 Dihedral : 7.850 93.052 1768 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.16 % Allowed : 22.83 % Favored : 72.01 % 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: -1.27 (0.21), residues: 1419 helix: -0.08 (0.17), residues: 861 sheet: -0.96 (0.46), residues: 120 loop : -2.21 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1290 TYR 0.023 0.002 TYR A1755 PHE 0.017 0.002 PHE A1740 TRP 0.015 0.002 TRP A1382 HIS 0.004 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00580 (11965) covalent geometry : angle 0.73921 (16214) SS BOND : bond 0.00681 ( 9) SS BOND : angle 1.70408 ( 18) hydrogen bonds : bond 0.04925 ( 746) hydrogen bonds : angle 5.10328 ( 2145) link_BETA1-4 : bond 0.00392 ( 2) link_BETA1-4 : angle 4.29711 ( 6) link_NAG-ASN : bond 0.00454 ( 7) link_NAG-ASN : angle 2.71433 ( 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 286 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 220 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7149 (mmtt) REVERT: A 820 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7572 (mm) REVERT: A 1236 ILE cc_start: 0.8573 (mt) cc_final: 0.8371 (mp) REVERT: A 1287 LYS cc_start: 0.8502 (tptp) cc_final: 0.8290 (tppt) REVERT: A 1305 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: A 1309 VAL cc_start: 0.8121 (p) cc_final: 0.7751 (m) REVERT: A 1349 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: A 1435 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7585 (pt) REVERT: A 1464 LYS cc_start: 0.7660 (tttm) cc_final: 0.7358 (ttmm) REVERT: A 1465 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8091 (pptt) REVERT: A 1466 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8083 (mtpt) REVERT: A 1518 ASP cc_start: 0.8322 (m-30) cc_final: 0.7894 (m-30) REVERT: A 1537 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: A 1541 GLN cc_start: 0.8314 (tp40) cc_final: 0.8092 (tp40) REVERT: A 1610 ARG cc_start: 0.6231 (mtp85) cc_final: 0.5768 (mtp180) REVERT: A 1665 ASN cc_start: 0.8301 (m110) cc_final: 0.8042 (m110) REVERT: A 1727 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 69 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8007 (ttpt) REVERT: B 99 LYS cc_start: 0.7340 (tptm) cc_final: 0.6913 (tppt) REVERT: B 154 MET cc_start: 0.6815 (mtt) cc_final: 0.6318 (mtm) REVERT: B 162 MET cc_start: 0.6647 (tpt) cc_final: 0.6403 (tpt) REVERT: B 182 TYR cc_start: 0.7878 (t80) cc_final: 0.7371 (t80) outliers start: 66 outliers final: 38 residues processed: 270 average time/residue: 0.1030 time to fit residues: 40.3025 Evaluate side-chains 256 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 285 THR 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 746 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 925 CYS 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 1315 ILE 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 1409 THR 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 1537 GLU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1608 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 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 138 optimal weight: 30.0000 chunk 67 optimal weight: 0.0030 chunk 16 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN A 265 GLN A1276 ASN A1528 ASN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.225129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.177903 restraints weight = 12471.001| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.17 r_work: 0.3637 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11983 Z= 0.137 Angle : 0.660 12.234 16259 Z= 0.331 Chirality : 0.043 0.277 1886 Planarity : 0.004 0.040 1978 Dihedral : 7.312 76.197 1766 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.07 % Rotamer: Outliers : 4.38 % Allowed : 23.53 % Favored : 72.09 % 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: -0.80 (0.21), residues: 1419 helix: 0.31 (0.17), residues: 859 sheet: -0.83 (0.47), residues: 117 loop : -2.03 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.022 0.001 TYR A1739 PHE 0.021 0.001 PHE A1197 TRP 0.016 0.001 TRP A 151 HIS 0.004 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00287 (11965) covalent geometry : angle 0.64449 (16214) SS BOND : bond 0.00432 ( 9) SS BOND : angle 1.08834 ( 18) hydrogen bonds : bond 0.04382 ( 746) hydrogen bonds : angle 4.86516 ( 2145) link_BETA1-4 : bond 0.00586 ( 2) link_BETA1-4 : angle 4.52962 ( 6) link_NAG-ASN : bond 0.00432 ( 7) link_NAG-ASN : angle 3.04192 ( 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 278 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.6543 (ttt90) cc_final: 0.6327 (ttt-90) REVERT: A 222 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8085 (mt) REVERT: A 300 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.7017 (mtt-85) REVERT: A 301 LYS cc_start: 0.7628 (mtmt) cc_final: 0.7177 (mmtt) REVERT: A 742 MET cc_start: 0.3579 (mmt) cc_final: 0.2247 (mtt) REVERT: A 820 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7614 (mm) REVERT: A 890 LYS cc_start: 0.7362 (mtpp) cc_final: 0.6952 (mmtt) REVERT: A 1254 PHE cc_start: 0.7431 (m-10) cc_final: 0.7182 (m-80) REVERT: A 1305 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: A 1309 VAL cc_start: 0.7959 (p) cc_final: 0.7673 (m) REVERT: A 1349 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.6991 (pm20) REVERT: A 1435 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7272 (pt) REVERT: A 1447 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7373 (t80) REVERT: A 1464 LYS cc_start: 0.7620 (tttm) cc_final: 0.7337 (ttmm) REVERT: A 1465 LYS cc_start: 0.8656 (mmmt) cc_final: 0.8079 (pptt) REVERT: A 1466 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8048 (mtpt) REVERT: A 1518 ASP cc_start: 0.8251 (m-30) cc_final: 0.7789 (m-30) REVERT: A 1541 GLN cc_start: 0.8302 (tp40) cc_final: 0.8093 (tp40) REVERT: A 1610 ARG cc_start: 0.6273 (mtp85) cc_final: 0.5899 (mtp180) REVERT: A 1727 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: B 69 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8030 (ttpt) REVERT: B 99 LYS cc_start: 0.7180 (tptm) cc_final: 0.6814 (tppt) REVERT: B 154 MET cc_start: 0.6715 (mtt) cc_final: 0.6317 (mtm) REVERT: B 162 MET cc_start: 0.6468 (tpt) cc_final: 0.6247 (tpt) REVERT: B 182 TYR cc_start: 0.7838 (t80) cc_final: 0.7382 (t80) outliers start: 56 outliers final: 29 residues processed: 262 average time/residue: 0.1020 time to fit residues: 38.6953 Evaluate side-chains 255 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 817 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 859 ILE 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 1234 THR 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 1385 LEU Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1447 PHE Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1608 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 74 GLU Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 0.0170 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A1276 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 = 0.4533 r_free = 0.4533 target = 0.224546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.178084 restraints weight = 12431.013| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.91 r_work: 0.3657 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2215 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= 0.150 Angle : 0.658 11.691 16259 Z= 0.333 Chirality : 0.043 0.272 1886 Planarity : 0.004 0.042 1978 Dihedral : 6.669 58.125 1766 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 5.00 % Allowed : 24.00 % Favored : 70.99 % 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: -0.60 (0.22), residues: 1419 helix: 0.44 (0.17), residues: 863 sheet: -0.32 (0.49), residues: 111 loop : -2.01 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1290 TYR 0.023 0.002 TYR A1482 PHE 0.021 0.001 PHE A1197 TRP 0.018 0.001 TRP A 151 HIS 0.003 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00327 (11965) covalent geometry : angle 0.64721 (16214) SS BOND : bond 0.00412 ( 9) SS BOND : angle 0.96321 ( 18) hydrogen bonds : bond 0.04329 ( 746) hydrogen bonds : angle 4.83237 ( 2145) link_BETA1-4 : bond 0.00121 ( 2) link_BETA1-4 : angle 4.45690 ( 6) link_NAG-ASN : bond 0.00380 ( 7) link_NAG-ASN : angle 2.34363 ( 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 288 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 224 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ARG cc_start: 0.7416 (ttm-80) cc_final: 0.7063 (mtt-85) REVERT: A 301 LYS cc_start: 0.7640 (mtmt) cc_final: 0.7224 (mmtt) REVERT: A 742 MET cc_start: 0.3655 (mmt) cc_final: 0.2400 (mtt) REVERT: A 768 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5947 (ttm) REVERT: A 890 LYS cc_start: 0.7430 (mtpp) cc_final: 0.7123 (mmtt) REVERT: A 969 SER cc_start: 0.5652 (OUTLIER) cc_final: 0.5355 (m) REVERT: A 1254 PHE cc_start: 0.7317 (m-10) cc_final: 0.7040 (m-80) REVERT: A 1287 LYS cc_start: 0.8369 (tppt) cc_final: 0.7562 (mtpt) REVERT: A 1305 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: A 1309 VAL cc_start: 0.8081 (p) cc_final: 0.7825 (m) REVERT: A 1349 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.6842 (pt0) REVERT: A 1435 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7305 (pt) REVERT: A 1447 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7363 (t80) REVERT: A 1465 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8088 (pptt) REVERT: A 1466 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8180 (mtpt) REVERT: A 1518 ASP cc_start: 0.8288 (m-30) cc_final: 0.7840 (m-30) REVERT: A 1540 SER cc_start: 0.7551 (t) cc_final: 0.7284 (m) REVERT: A 1541 GLN cc_start: 0.8330 (tp40) cc_final: 0.7667 (tp40) REVERT: A 1610 ARG cc_start: 0.6503 (mtp85) cc_final: 0.6176 (mtp180) REVERT: A 1727 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 69 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8101 (ttpt) REVERT: B 99 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6819 (tppt) REVERT: B 152 ARG cc_start: 0.8023 (ptm160) cc_final: 0.6692 (ptm-80) REVERT: B 154 MET cc_start: 0.6608 (mtt) cc_final: 0.6189 (mtm) REVERT: B 160 GLU cc_start: 0.7477 (tt0) cc_final: 0.7197 (tt0) REVERT: B 162 MET cc_start: 0.6488 (tpt) cc_final: 0.6262 (tpt) REVERT: B 182 TYR cc_start: 0.7771 (t80) cc_final: 0.7384 (t80) outliers start: 64 outliers final: 30 residues processed: 267 average time/residue: 0.0955 time to fit residues: 37.2167 Evaluate side-chains 251 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 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 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 768 MET Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 969 SER 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 1385 LEU 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 1508 ILE Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1608 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 1730 CYS 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 99 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 0.0470 chunk 100 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 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 = 0.4546 r_free = 0.4546 target = 0.226267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.179486 restraints weight = 12512.248| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.73 r_work: 0.3684 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2473 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= 0.136 Angle : 0.644 11.107 16259 Z= 0.325 Chirality : 0.043 0.286 1886 Planarity : 0.004 0.041 1978 Dihedral : 6.250 57.938 1764 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.61 % Allowed : 24.86 % Favored : 70.52 % 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: 0.56 (0.17), residues: 862 sheet: -0.66 (0.46), residues: 126 loop : -1.80 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.020 0.001 TYR A1436 PHE 0.029 0.001 PHE A1197 TRP 0.020 0.001 TRP A 151 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00284 (11965) covalent geometry : angle 0.63184 (16214) SS BOND : bond 0.00356 ( 9) SS BOND : angle 0.73704 ( 18) hydrogen bonds : bond 0.04236 ( 746) hydrogen bonds : angle 4.77427 ( 2145) link_BETA1-4 : bond 0.00215 ( 2) link_BETA1-4 : angle 3.95717 ( 6) link_NAG-ASN : bond 0.00706 ( 7) link_NAG-ASN : angle 2.79670 ( 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 277 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8612 (mp) REVERT: A 164 THR cc_start: 0.8660 (t) cc_final: 0.8330 (p) REVERT: A 300 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6939 (mtt-85) REVERT: A 301 LYS cc_start: 0.7520 (mtmt) cc_final: 0.7159 (mmtt) REVERT: A 742 MET cc_start: 0.3745 (mmt) cc_final: 0.2506 (mtt) REVERT: A 768 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5949 (ttm) REVERT: A 820 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7239 (mm) REVERT: A 890 LYS cc_start: 0.7459 (mtpp) cc_final: 0.7083 (mmtt) REVERT: A 1254 PHE cc_start: 0.7340 (m-10) cc_final: 0.6980 (m-80) REVERT: A 1287 LYS cc_start: 0.8262 (tppt) cc_final: 0.7691 (mtpp) REVERT: A 1305 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: A 1309 VAL cc_start: 0.7989 (p) cc_final: 0.7741 (m) REVERT: A 1349 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6863 (pt0) REVERT: A 1435 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7266 (pt) REVERT: A 1465 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8090 (pptt) REVERT: A 1466 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8150 (mtpt) REVERT: A 1518 ASP cc_start: 0.8298 (m-30) cc_final: 0.7836 (m-30) REVERT: A 1540 SER cc_start: 0.7601 (t) cc_final: 0.7354 (m) REVERT: A 1541 GLN cc_start: 0.8300 (tp40) cc_final: 0.7639 (tp40) REVERT: A 1565 LYS cc_start: 0.8688 (pttm) cc_final: 0.8088 (ptpt) REVERT: A 1610 ARG cc_start: 0.6543 (mtp85) cc_final: 0.6289 (mtp180) REVERT: A 1658 TYR cc_start: 0.8242 (m-80) cc_final: 0.7915 (m-80) REVERT: A 1727 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7199 (mt-10) REVERT: B 69 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7920 (ttpt) REVERT: B 99 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6790 (tppt) REVERT: B 154 MET cc_start: 0.6647 (mtt) cc_final: 0.6251 (mtm) REVERT: B 160 GLU cc_start: 0.7447 (tt0) cc_final: 0.7089 (tt0) REVERT: B 162 MET cc_start: 0.6513 (tpt) cc_final: 0.6276 (tpt) REVERT: B 182 TYR cc_start: 0.7793 (t80) cc_final: 0.7499 (t80) outliers start: 59 outliers final: 34 residues processed: 260 average time/residue: 0.0935 time to fit residues: 35.8652 Evaluate side-chains 251 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 172 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 346 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 LEU 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 1243 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 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 1575 THR 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 1701 ASP 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 99 LYS 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: 10.0000 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 395 ASN A1579 ASN ** 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 = 0.4531 r_free = 0.4531 target = 0.224471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175775 restraints weight = 12526.263| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.33 r_work: 0.3667 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11983 Z= 0.159 Angle : 0.655 11.674 16259 Z= 0.330 Chirality : 0.043 0.289 1886 Planarity : 0.004 0.040 1978 Dihedral : 6.099 58.964 1760 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.22 % Allowed : 24.78 % Favored : 70.99 % 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: -0.33 (0.22), residues: 1419 helix: 0.63 (0.17), residues: 859 sheet: -0.52 (0.46), residues: 126 loop : -1.77 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.021 0.001 TYR A1482 PHE 0.018 0.001 PHE A1740 TRP 0.021 0.001 TRP A 151 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00358 (11965) covalent geometry : angle 0.64495 (16214) SS BOND : bond 0.00506 ( 9) SS BOND : angle 0.83538 ( 18) hydrogen bonds : bond 0.04234 ( 746) hydrogen bonds : angle 4.80189 ( 2145) link_BETA1-4 : bond 0.00176 ( 2) link_BETA1-4 : angle 3.76340 ( 6) link_NAG-ASN : bond 0.00242 ( 7) link_NAG-ASN : angle 2.48496 ( 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: 54 poor density : 213 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 164 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8339 (p) REVERT: A 222 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7977 (mt) REVERT: A 300 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.6951 (mtt-85) REVERT: A 301 LYS cc_start: 0.7534 (mtmt) cc_final: 0.7074 (mmtt) REVERT: A 742 MET cc_start: 0.3648 (mmt) cc_final: 0.2485 (mtt) REVERT: A 768 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5943 (ttm) REVERT: A 890 LYS cc_start: 0.7473 (mtpp) cc_final: 0.7113 (mmtt) REVERT: A 946 ILE cc_start: 0.8571 (mt) cc_final: 0.8272 (mp) REVERT: A 969 SER cc_start: 0.5780 (OUTLIER) cc_final: 0.5462 (m) REVERT: A 1254 PHE cc_start: 0.7321 (m-10) cc_final: 0.6984 (m-80) REVERT: A 1287 LYS cc_start: 0.8251 (tppt) cc_final: 0.7682 (mtpp) REVERT: A 1305 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: A 1309 VAL cc_start: 0.7920 (p) cc_final: 0.7656 (m) REVERT: A 1349 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.6902 (pt0) REVERT: A 1435 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7277 (pt) REVERT: A 1518 ASP cc_start: 0.8339 (m-30) cc_final: 0.7871 (m-30) REVERT: A 1540 SER cc_start: 0.7547 (t) cc_final: 0.7288 (m) REVERT: A 1541 GLN cc_start: 0.8268 (tp40) cc_final: 0.7603 (tp40) REVERT: A 1610 ARG cc_start: 0.6474 (mtp85) cc_final: 0.6239 (mtp180) REVERT: A 1665 ASN cc_start: 0.8046 (m110) cc_final: 0.7172 (m110) REVERT: A 1727 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: A 1739 TYR cc_start: 0.7723 (t80) cc_final: 0.7399 (t80) REVERT: A 1741 VAL cc_start: 0.8653 (t) cc_final: 0.8394 (t) REVERT: B 69 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8124 (ttpt) REVERT: B 99 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6778 (tppt) REVERT: B 154 MET cc_start: 0.6612 (mtt) cc_final: 0.6248 (mtm) REVERT: B 160 GLU cc_start: 0.7375 (tt0) cc_final: 0.7045 (tt0) REVERT: B 162 MET cc_start: 0.6406 (tpt) cc_final: 0.6196 (tpt) REVERT: B 182 TYR cc_start: 0.7716 (t80) cc_final: 0.7415 (t80) outliers start: 54 outliers final: 33 residues processed: 250 average time/residue: 0.0951 time to fit residues: 34.8141 Evaluate side-chains 252 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 364 GLU Chi-restraints excluded: chain A residue 377 THR 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 969 SER 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 1243 LEU 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 1351 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER 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 1482 TYR Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1672 GLU Chi-restraints excluded: chain A residue 1701 ASP 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 1730 CYS Chi-restraints excluded: chain A residue 1734 SER 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 99 LYS Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 83 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 780 ASN 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 = 0.4528 r_free = 0.4528 target = 0.223864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.179765 restraints weight = 12481.534| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.80 r_work: 0.3650 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11983 Z= 0.159 Angle : 0.658 11.670 16259 Z= 0.331 Chirality : 0.044 0.290 1886 Planarity : 0.004 0.040 1978 Dihedral : 5.974 58.727 1758 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.77 % Allowed : 25.02 % 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: -0.28 (0.22), residues: 1419 helix: 0.65 (0.17), residues: 863 sheet: -0.42 (0.47), residues: 126 loop : -1.73 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.024 0.001 TYR A1348 PHE 0.028 0.001 PHE A1197 TRP 0.025 0.001 TRP A 151 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00357 (11965) covalent geometry : angle 0.64623 (16214) SS BOND : bond 0.00470 ( 9) SS BOND : angle 1.05587 ( 18) hydrogen bonds : bond 0.04220 ( 746) hydrogen bonds : angle 4.82147 ( 2145) link_BETA1-4 : bond 0.00129 ( 2) link_BETA1-4 : angle 3.57832 ( 6) link_NAG-ASN : bond 0.00348 ( 7) link_NAG-ASN : angle 2.85900 ( 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 269 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8530 (mp) REVERT: A 164 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 222 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7772 (mt) REVERT: A 300 ARG cc_start: 0.7371 (ttm-80) cc_final: 0.6925 (mtt-85) REVERT: A 301 LYS cc_start: 0.7512 (mtmt) cc_final: 0.7062 (mmtt) REVERT: A 742 MET cc_start: 0.3664 (mmt) cc_final: 0.2508 (mtt) REVERT: A 768 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5888 (ttm) REVERT: A 890 LYS cc_start: 0.7492 (mtpp) cc_final: 0.7105 (mmtt) REVERT: A 946 ILE cc_start: 0.8546 (mt) cc_final: 0.8229 (mp) REVERT: A 969 SER cc_start: 0.5806 (OUTLIER) cc_final: 0.5485 (m) REVERT: A 1254 PHE cc_start: 0.7337 (m-10) cc_final: 0.6991 (m-80) REVERT: A 1287 LYS cc_start: 0.8282 (tppt) cc_final: 0.7712 (mtpp) REVERT: A 1305 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: A 1309 VAL cc_start: 0.7935 (p) cc_final: 0.7669 (m) REVERT: A 1349 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.6932 (pt0) REVERT: A 1435 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7298 (pt) REVERT: A 1447 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7350 (t80) REVERT: A 1540 SER cc_start: 0.7576 (t) cc_final: 0.7317 (m) REVERT: A 1541 GLN cc_start: 0.8273 (tp40) cc_final: 0.7917 (tp40) REVERT: A 1610 ARG cc_start: 0.6573 (mtp85) cc_final: 0.6362 (mtp180) REVERT: A 1658 TYR cc_start: 0.8323 (m-80) cc_final: 0.8098 (m-80) REVERT: A 1665 ASN cc_start: 0.8074 (m110) cc_final: 0.7283 (m110) REVERT: A 1727 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: B 69 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8137 (ttpt) REVERT: B 87 GLU cc_start: 0.7595 (tt0) cc_final: 0.7341 (mt-10) REVERT: B 99 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6767 (tppt) REVERT: B 152 ARG cc_start: 0.8251 (ptm160) cc_final: 0.7375 (ptm-80) REVERT: B 154 MET cc_start: 0.6657 (mtt) cc_final: 0.6261 (mtm) REVERT: B 160 GLU cc_start: 0.7405 (tt0) cc_final: 0.7046 (tt0) REVERT: B 162 MET cc_start: 0.6438 (tpt) cc_final: 0.6223 (tpt) REVERT: B 182 TYR cc_start: 0.7693 (t80) cc_final: 0.7391 (t80) outliers start: 61 outliers final: 38 residues processed: 247 average time/residue: 0.1008 time to fit residues: 36.3411 Evaluate side-chains 254 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 364 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 750 ILE 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 969 SER 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 1243 LEU 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 1376 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1390 ASP 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 1575 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1672 GLU Chi-restraints excluded: chain A residue 1701 ASP 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 1730 CYS Chi-restraints excluded: chain A residue 1734 SER 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 70 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS 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: 0.1980 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.225468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177571 restraints weight = 12343.989| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 3.51 r_work: 0.3693 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2853 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= 0.138 Angle : 0.655 13.129 16259 Z= 0.330 Chirality : 0.043 0.291 1886 Planarity : 0.004 0.042 1978 Dihedral : 5.907 59.441 1756 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.22 % Allowed : 25.65 % Favored : 70.13 % 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: -0.18 (0.22), residues: 1419 helix: 0.76 (0.17), residues: 862 sheet: -0.40 (0.46), residues: 126 loop : -1.76 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 214 TYR 0.023 0.001 TYR A1348 PHE 0.025 0.001 PHE A1666 TRP 0.028 0.001 TRP A 151 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00299 (11965) covalent geometry : angle 0.63942 (16214) SS BOND : bond 0.00922 ( 9) SS BOND : angle 2.20283 ( 18) hydrogen bonds : bond 0.04116 ( 746) hydrogen bonds : angle 4.77031 ( 2145) link_BETA1-4 : bond 0.00115 ( 2) link_BETA1-4 : angle 3.39397 ( 6) link_NAG-ASN : bond 0.00301 ( 7) link_NAG-ASN : angle 2.99318 ( 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 267 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 213 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8500 (mp) REVERT: A 164 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8343 (p) REVERT: A 222 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7724 (mt) REVERT: A 300 ARG cc_start: 0.7271 (ttm-80) cc_final: 0.6832 (mtt-85) REVERT: A 301 LYS cc_start: 0.7512 (mtmt) cc_final: 0.7039 (mmtt) REVERT: A 742 MET cc_start: 0.3698 (mmt) cc_final: 0.2608 (mtt) REVERT: A 768 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.6030 (ttm) REVERT: A 890 LYS cc_start: 0.7409 (mtpp) cc_final: 0.7040 (mmtt) REVERT: A 946 ILE cc_start: 0.8543 (mt) cc_final: 0.8226 (mp) REVERT: A 969 SER cc_start: 0.5707 (OUTLIER) cc_final: 0.5441 (m) REVERT: A 1254 PHE cc_start: 0.7256 (m-10) cc_final: 0.6885 (m-80) REVERT: A 1287 LYS cc_start: 0.8276 (tppt) cc_final: 0.7787 (mttp) REVERT: A 1305 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: A 1309 VAL cc_start: 0.7831 (p) cc_final: 0.7615 (m) REVERT: A 1349 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6940 (pt0) REVERT: A 1435 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7235 (pt) REVERT: A 1447 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7355 (t80) REVERT: A 1540 SER cc_start: 0.7544 (t) cc_final: 0.7290 (m) REVERT: A 1541 GLN cc_start: 0.8297 (tp40) cc_final: 0.7932 (tp40) REVERT: A 1610 ARG cc_start: 0.6545 (mtp85) cc_final: 0.6339 (mtp180) REVERT: A 1727 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: B 69 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8186 (ttpt) REVERT: B 81 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6323 (mp0) REVERT: B 99 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6757 (tppt) REVERT: B 160 GLU cc_start: 0.7339 (tt0) cc_final: 0.6920 (tt0) REVERT: B 162 MET cc_start: 0.6394 (tpt) cc_final: 0.6179 (tpt) REVERT: B 182 TYR cc_start: 0.7714 (t80) cc_final: 0.7407 (t80) REVERT: F 85 MET cc_start: 0.2684 (mmm) cc_final: 0.1972 (mmm) outliers start: 54 outliers final: 34 residues processed: 249 average time/residue: 0.1012 time to fit residues: 36.7472 Evaluate side-chains 256 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 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 247 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 364 GLU 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 969 SER 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 1243 LEU 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 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 1524 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1672 GLU Chi-restraints excluded: chain A residue 1701 ASP 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 1730 CYS Chi-restraints excluded: chain A residue 1734 SER 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 99 LYS 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: 0.9990 chunk 127 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.224971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.177649 restraints weight = 12524.916| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.81 r_work: 0.3686 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 0.070 11983 Z= 0.147 Angle : 0.668 12.145 16259 Z= 0.335 Chirality : 0.043 0.288 1886 Planarity : 0.004 0.039 1978 Dihedral : 5.922 57.559 1754 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.07 % Allowed : 25.96 % Favored : 69.98 % 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: -0.12 (0.22), residues: 1419 helix: 0.80 (0.17), residues: 859 sheet: -0.38 (0.46), residues: 126 loop : -1.71 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 217 TYR 0.051 0.002 TYR A1739 PHE 0.030 0.001 PHE A1197 TRP 0.028 0.001 TRP A 151 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00325 (11965) covalent geometry : angle 0.65125 (16214) SS BOND : bond 0.00762 ( 9) SS BOND : angle 1.98239 ( 18) hydrogen bonds : bond 0.04137 ( 746) hydrogen bonds : angle 4.81291 ( 2145) link_BETA1-4 : bond 0.00101 ( 2) link_BETA1-4 : angle 3.24368 ( 6) link_NAG-ASN : bond 0.00369 ( 7) link_NAG-ASN : angle 3.34867 ( 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 266 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 164 THR cc_start: 0.8671 (t) cc_final: 0.8381 (p) REVERT: A 222 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 300 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.6880 (mtt-85) REVERT: A 301 LYS cc_start: 0.7525 (mtmt) cc_final: 0.7075 (mmtt) REVERT: A 742 MET cc_start: 0.3774 (mmt) cc_final: 0.2600 (mtp) REVERT: A 768 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5924 (ttm) REVERT: A 890 LYS cc_start: 0.7512 (mtpp) cc_final: 0.7069 (mmtt) REVERT: A 946 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 969 SER cc_start: 0.5849 (OUTLIER) cc_final: 0.5619 (m) REVERT: A 1254 PHE cc_start: 0.7196 (m-10) cc_final: 0.6810 (m-80) REVERT: A 1305 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: A 1309 VAL cc_start: 0.7894 (p) cc_final: 0.7691 (m) REVERT: A 1349 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.6786 (pm20) REVERT: A 1435 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7261 (pt) REVERT: A 1447 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 1540 SER cc_start: 0.7668 (t) cc_final: 0.7415 (m) REVERT: A 1541 GLN cc_start: 0.8248 (tp40) cc_final: 0.7908 (tp40) REVERT: A 1565 LYS cc_start: 0.8917 (pttm) cc_final: 0.8261 (ptpt) REVERT: A 1665 ASN cc_start: 0.8079 (m110) cc_final: 0.6789 (m110) REVERT: A 1727 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: B 69 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8247 (ttpt) REVERT: B 81 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6338 (mp0) REVERT: B 87 GLU cc_start: 0.7507 (tt0) cc_final: 0.7262 (mt-10) REVERT: B 99 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6805 (tppt) REVERT: B 152 ARG cc_start: 0.8176 (ptm160) cc_final: 0.7290 (ptt90) REVERT: B 160 GLU cc_start: 0.7338 (tt0) cc_final: 0.6873 (tt0) REVERT: B 162 MET cc_start: 0.6536 (tpt) cc_final: 0.6261 (tpt) REVERT: B 182 TYR cc_start: 0.7720 (t80) cc_final: 0.7422 (t80) outliers start: 52 outliers final: 34 residues processed: 247 average time/residue: 0.0959 time to fit residues: 34.6413 Evaluate side-chains 257 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE 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 364 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE 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 946 ILE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 969 SER 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 1243 LEU 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 1351 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER 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 1575 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1672 GLU Chi-restraints excluded: chain A residue 1701 ASP 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 1730 CYS 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 99 LYS 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: 4.9990 chunk 115 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN 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 = 0.4528 r_free = 0.4528 target = 0.224150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.177174 restraints weight = 12459.765| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.73 r_work: 0.3692 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11983 Z= 0.165 Angle : 0.741 23.902 16259 Z= 0.358 Chirality : 0.047 0.618 1886 Planarity : 0.004 0.040 1978 Dihedral : 6.292 58.050 1754 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.83 % Allowed : 26.04 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1419 helix: 0.74 (0.17), residues: 859 sheet: -0.42 (0.47), residues: 126 loop : -1.76 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 217 TYR 0.056 0.002 TYR A1739 PHE 0.021 0.001 PHE A1740 TRP 0.026 0.001 TRP A 151 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00375 (11965) covalent geometry : angle 0.68169 (16214) SS BOND : bond 0.00838 ( 9) SS BOND : angle 1.87114 ( 18) hydrogen bonds : bond 0.04198 ( 746) hydrogen bonds : angle 4.81988 ( 2145) link_BETA1-4 : bond 0.00117 ( 2) link_BETA1-4 : angle 3.17093 ( 6) link_NAG-ASN : bond 0.00737 ( 7) link_NAG-ASN : angle 7.80534 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.05 seconds wall clock time: 59 minutes 10.23 seconds (3550.23 seconds total)