Starting phenix.real_space_refine on Wed Jul 30 16:47:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xmg_33296/07_2025/7xmg_33296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmg_33296/07_2025/7xmg_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_33296/07_2025/7xmg_33296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmg_33296/07_2025/7xmg_33296.map" model { file = "/net/cci-nas-00/data/ceres_data/7xmg_33296/07_2025/7xmg_33296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmg_33296/07_2025/7xmg_33296.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG: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: 6.77, per 1000 atoms: 0.58 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: 3.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.25 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: 3.74 Time building geometry restraints manager: 3.71 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.520 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- 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 : 20.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.002 TRP A1382 HIS 0.004 0.001 HIS A 765 PHE 0.019 0.002 PHE F 80 TYR 0.022 0.002 TYR A1482 ARG 0.003 0.000 ARG F 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 7) link_NAG-ASN : angle 2.55441 ( 21) link_BETA1-4 : bond 0.00162 ( 2) link_BETA1-4 : angle 4.50437 ( 6) hydrogen bonds : bond 0.10118 ( 746) hydrogen bonds : angle 4.82408 ( 2145) SS BOND : bond 0.29796 ( 9) SS BOND : angle 19.29465 ( 18) covalent geometry : bond 0.00607 (11965) covalent geometry : angle 0.84721 (16214) *********************** 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 : 1.312 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: 0.7832 (OUTLIER) cc_final: 0.6685 (pt0) REVERT: A 1435 ILE cc_start: 0.7461 (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: 0.8047 (OUTLIER) cc_final: 0.7305 (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: 0.2310 time to fit residues: 103.4749 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 : 1.350 ------------------------------------------------------------------------------- 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 119 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 146 ASN A 240 GLN A 365 ASN A 410 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.225373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.180111 restraints weight = 12462.481| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.69 r_work: 0.3677 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11983 Z= 0.157 Angle : 0.712 14.829 16259 Z= 0.358 Chirality : 0.044 0.286 1886 Planarity : 0.004 0.054 1978 Dihedral : 9.496 108.636 1815 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.05 % Allowed : 23.46 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.21), residues: 1419 helix: -0.32 (0.16), residues: 863 sheet: -0.84 (0.49), residues: 117 loop : -2.27 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 151 HIS 0.004 0.001 HIS B 134 PHE 0.020 0.001 PHE A 165 TYR 0.025 0.002 TYR A1739 ARG 0.008 0.001 ARG F 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 7) link_NAG-ASN : angle 2.64366 ( 21) link_BETA1-4 : bond 0.00227 ( 2) link_BETA1-4 : angle 4.12168 ( 6) hydrogen bonds : bond 0.04744 ( 746) hydrogen bonds : angle 4.90261 ( 2145) SS BOND : bond 0.00610 ( 9) SS BOND : angle 2.09451 ( 18) covalent geometry : bond 0.00339 (11965) covalent geometry : angle 0.69852 (16214) *********************** 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 271 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 300 ARG cc_start: 0.7336 (ttm-80) cc_final: 0.6990 (mtt-85) REVERT: A 301 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7323 (mmtt) REVERT: A 742 MET cc_start: 0.5141 (mmm) cc_final: 0.3453 (mtp) REVERT: A 820 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7492 (mm) REVERT: A 927 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6961 (mt-10) REVERT: A 1236 ILE cc_start: 0.8588 (mt) cc_final: 0.8365 (mp) REVERT: A 1287 LYS cc_start: 0.8471 (tptp) cc_final: 0.8264 (tppt) REVERT: A 1305 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: A 1309 VAL cc_start: 0.8091 (p) cc_final: 0.7819 (m) REVERT: A 1349 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: A 1435 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7405 (pt) REVERT: A 1464 LYS cc_start: 0.7742 (tttm) cc_final: 0.7506 (ttmm) REVERT: A 1465 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8130 (pptt) REVERT: A 1466 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8100 (mtpt) REVERT: A 1474 MET cc_start: 0.7431 (mtt) cc_final: 0.7212 (mtm) REVERT: A 1518 ASP cc_start: 0.8229 (m-30) cc_final: 0.7811 (m-30) REVERT: A 1541 GLN cc_start: 0.8405 (tp40) cc_final: 0.8182 (tp40) REVERT: A 1565 LYS cc_start: 0.8746 (pttm) cc_final: 0.8308 (ptpp) REVERT: A 1658 TYR cc_start: 0.8231 (m-80) cc_final: 0.7993 (m-80) REVERT: A 1732 ASN cc_start: 0.7491 (t0) cc_final: 0.7244 (t0) REVERT: B 34 MET cc_start: 0.6148 (mmm) cc_final: 0.5913 (mmt) REVERT: B 69 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8036 (ttpt) REVERT: B 99 LYS cc_start: 0.7249 (tptm) cc_final: 0.6970 (tppt) REVERT: B 162 MET cc_start: 0.6640 (tpt) cc_final: 0.6385 (tpt) REVERT: B 182 TYR cc_start: 0.7829 (t80) cc_final: 0.7386 (t80) outliers start: 39 outliers final: 20 residues processed: 263 average time/residue: 0.2469 time to fit residues: 93.7470 Evaluate side-chains 242 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 780 ASN A 961 ASN A1276 ASN ** A1528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.223795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.178573 restraints weight = 12629.916| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.91 r_work: 0.3641 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11983 Z= 0.177 Angle : 0.690 15.761 16259 Z= 0.345 Chirality : 0.044 0.276 1886 Planarity : 0.004 0.044 1978 Dihedral : 7.874 95.200 1770 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.46 % Allowed : 23.22 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1419 helix: 0.03 (0.17), residues: 866 sheet: -0.96 (0.47), residues: 120 loop : -2.14 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 151 HIS 0.004 0.001 HIS A 766 PHE 0.014 0.001 PHE A 913 TYR 0.022 0.002 TYR A1739 ARG 0.005 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 7) link_NAG-ASN : angle 2.24951 ( 21) link_BETA1-4 : bond 0.00399 ( 2) link_BETA1-4 : angle 4.21799 ( 6) hydrogen bonds : bond 0.04600 ( 746) hydrogen bonds : angle 4.92764 ( 2145) SS BOND : bond 0.00517 ( 9) SS BOND : angle 1.38367 ( 18) covalent geometry : bond 0.00401 (11965) covalent geometry : angle 0.67977 (16214) *********************** 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 277 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ILE cc_start: 0.6999 (pt) cc_final: 0.6750 (mt) REVERT: A 300 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.7144 (mtt-85) REVERT: A 301 LYS cc_start: 0.7730 (mtmt) cc_final: 0.7273 (mmtt) REVERT: A 798 MET cc_start: 0.4218 (ptm) cc_final: 0.3970 (ptp) REVERT: A 820 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7585 (mm) REVERT: A 1236 ILE cc_start: 0.8533 (mt) cc_final: 0.8329 (mp) REVERT: A 1287 LYS cc_start: 0.8501 (tptp) cc_final: 0.8299 (tppt) REVERT: A 1305 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: A 1309 VAL cc_start: 0.8135 (p) cc_final: 0.7838 (m) REVERT: A 1349 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7051 (pm20) REVERT: A 1435 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7390 (pt) REVERT: A 1464 LYS cc_start: 0.7718 (tttm) cc_final: 0.7517 (ttmm) REVERT: A 1465 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8126 (pptt) REVERT: A 1466 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8090 (mtpt) REVERT: A 1518 ASP cc_start: 0.8277 (m-30) cc_final: 0.7832 (m-30) REVERT: A 1541 GLN cc_start: 0.8306 (tp40) cc_final: 0.8101 (tp40) REVERT: A 1610 ARG cc_start: 0.6066 (mtp85) cc_final: 0.5721 (mtp180) REVERT: A 1665 ASN cc_start: 0.8108 (m-40) cc_final: 0.7670 (m110) REVERT: A 1727 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: B 69 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8019 (ttpt) REVERT: B 99 LYS cc_start: 0.7296 (tptm) cc_final: 0.6958 (tppt) REVERT: B 154 MET cc_start: 0.6781 (mtt) cc_final: 0.6274 (mtm) REVERT: B 162 MET cc_start: 0.6680 (tpt) cc_final: 0.6414 (tpt) REVERT: B 182 TYR cc_start: 0.7859 (t80) cc_final: 0.7348 (t80) outliers start: 57 outliers final: 24 residues processed: 260 average time/residue: 0.3698 time to fit residues: 141.1537 Evaluate side-chains 242 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1390 ASP Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 135 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 A 911 ASN A1276 ASN A1528 ASN A1579 ASN B 102 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.221242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.172758 restraints weight = 12432.813| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.83 r_work: 0.3547 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11983 Z= 0.221 Angle : 0.719 14.242 16259 Z= 0.361 Chirality : 0.046 0.297 1886 Planarity : 0.004 0.042 1978 Dihedral : 7.315 72.046 1766 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.94 % Allowed : 21.89 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1419 helix: 0.14 (0.17), residues: 856 sheet: -0.50 (0.49), residues: 108 loop : -2.16 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 151 HIS 0.004 0.001 HIS A 766 PHE 0.021 0.002 PHE A1740 TYR 0.019 0.002 TYR A 367 ARG 0.006 0.001 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 7) link_NAG-ASN : angle 3.11863 ( 21) link_BETA1-4 : bond 0.00119 ( 2) link_BETA1-4 : angle 4.64133 ( 6) hydrogen bonds : bond 0.04717 ( 746) hydrogen bonds : angle 5.03182 ( 2145) SS BOND : bond 0.00787 ( 9) SS BOND : angle 1.44878 ( 18) covalent geometry : bond 0.00515 (11965) covalent geometry : angle 0.70417 (16214) *********************** 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 299 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 223 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7227 (mmtt) REVERT: A 742 MET cc_start: 0.3569 (mmt) cc_final: 0.2207 (mtp) REVERT: A 760 PHE cc_start: 0.7620 (t80) cc_final: 0.7418 (m-80) REVERT: A 798 MET cc_start: 0.4144 (ptm) cc_final: 0.3918 (ptm) REVERT: A 820 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7557 (mm) REVERT: A 1305 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: A 1309 VAL cc_start: 0.8004 (p) cc_final: 0.7653 (m) REVERT: A 1349 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7112 (pm20) REVERT: A 1435 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7397 (pt) REVERT: A 1447 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7396 (t80) REVERT: A 1464 LYS cc_start: 0.7646 (tttm) cc_final: 0.7329 (ttmm) REVERT: A 1465 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8097 (pptt) REVERT: A 1466 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8131 (mtpt) REVERT: A 1518 ASP cc_start: 0.8287 (m-30) cc_final: 0.7834 (m-30) REVERT: A 1541 GLN cc_start: 0.8357 (tp40) cc_final: 0.8135 (tp40) REVERT: A 1610 ARG cc_start: 0.6085 (mtp85) cc_final: 0.5783 (mtp180) REVERT: A 1727 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: B 69 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8084 (ttpt) REVERT: B 99 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6820 (tppt) REVERT: B 154 MET cc_start: 0.6630 (mtt) cc_final: 0.6247 (mtm) REVERT: B 162 MET cc_start: 0.6455 (tpt) cc_final: 0.6210 (tpt) REVERT: B 182 TYR cc_start: 0.7851 (t80) cc_final: 0.7362 (t80) outliers start: 76 outliers final: 48 residues processed: 280 average time/residue: 0.2268 time to fit residues: 91.3702 Evaluate side-chains 267 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 211 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 172 LEU 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 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 859 ILE 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 1234 THR Chi-restraints excluded: chain A residue 1238 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 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 1385 LEU 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 1447 PHE Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1497 ILE 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 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU 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 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 Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 137 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 93 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** 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 = 0.4534 r_free = 0.4534 target = 0.224768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.180941 restraints weight = 12454.096| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.72 r_work: 0.3651 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2184 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= 0.141 Angle : 0.654 11.290 16259 Z= 0.330 Chirality : 0.043 0.276 1886 Planarity : 0.004 0.040 1978 Dihedral : 6.625 58.810 1764 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.53 % Allowed : 24.32 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1419 helix: 0.41 (0.17), residues: 859 sheet: -0.78 (0.45), residues: 123 loop : -1.96 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 151 HIS 0.004 0.001 HIS B 134 PHE 0.019 0.001 PHE A1197 TYR 0.021 0.001 TYR A1739 ARG 0.006 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 7) link_NAG-ASN : angle 2.92256 ( 21) link_BETA1-4 : bond 0.00180 ( 2) link_BETA1-4 : angle 4.50401 ( 6) hydrogen bonds : bond 0.04330 ( 746) hydrogen bonds : angle 4.85292 ( 2145) SS BOND : bond 0.00572 ( 9) SS BOND : angle 1.06327 ( 18) covalent geometry : bond 0.00302 (11965) covalent geometry : angle 0.63919 (16214) *********************** 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 279 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8263 (p) REVERT: A 222 LEU cc_start: 0.8297 (mt) cc_final: 0.8079 (mt) REVERT: A 300 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7081 (mtt-85) REVERT: A 301 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7270 (mmtt) REVERT: A 742 MET cc_start: 0.3747 (mmt) cc_final: 0.2513 (mtp) REVERT: A 798 MET cc_start: 0.4189 (ptm) cc_final: 0.3908 (ptm) REVERT: A 890 LYS cc_start: 0.7456 (mtpp) cc_final: 0.7227 (mmtt) REVERT: A 969 SER cc_start: 0.5765 (OUTLIER) cc_final: 0.5465 (m) REVERT: A 1201 MET cc_start: 0.8034 (tpp) cc_final: 0.7732 (tpp) REVERT: A 1254 PHE cc_start: 0.7364 (m-10) cc_final: 0.7108 (m-80) REVERT: A 1287 LYS cc_start: 0.8366 (tppt) cc_final: 0.7567 (mtpt) REVERT: A 1305 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: A 1309 VAL cc_start: 0.8078 (p) cc_final: 0.7798 (m) REVERT: A 1349 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: A 1435 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7319 (pt) REVERT: A 1610 ARG cc_start: 0.6353 (mtp85) cc_final: 0.6102 (mtp180) REVERT: A 1663 MET cc_start: 0.8839 (mtp) cc_final: 0.8603 (mtp) REVERT: A 1714 ASP cc_start: 0.6914 (m-30) cc_final: 0.6687 (m-30) REVERT: A 1727 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: B 69 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8090 (ttpt) REVERT: B 72 ARG cc_start: 0.7592 (ttt90) cc_final: 0.7352 (ttt-90) REVERT: B 99 LYS cc_start: 0.7224 (tptm) cc_final: 0.6869 (tppt) REVERT: B 152 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7827 (ptm-80) REVERT: B 154 MET cc_start: 0.6699 (mtt) cc_final: 0.6285 (mtm) REVERT: B 160 GLU cc_start: 0.7527 (tt0) cc_final: 0.7206 (tt0) REVERT: B 162 MET cc_start: 0.6613 (tpt) cc_final: 0.6387 (tpt) REVERT: B 182 TYR cc_start: 0.7806 (t80) cc_final: 0.7406 (t80) outliers start: 58 outliers final: 28 residues processed: 263 average time/residue: 0.2554 time to fit residues: 97.0623 Evaluate side-chains 249 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 164 THR 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 746 VAL Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 925 CYS 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 1388 ASN 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 1497 ILE Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 44 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A1541 GLN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.224548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.177699 restraints weight = 12542.904| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.95 r_work: 0.3678 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2379 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= 0.141 Angle : 0.636 11.530 16259 Z= 0.321 Chirality : 0.043 0.288 1886 Planarity : 0.004 0.040 1978 Dihedral : 6.272 58.162 1762 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.46 % Allowed : 24.78 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1419 helix: 0.54 (0.17), residues: 861 sheet: -0.71 (0.45), residues: 126 loop : -1.79 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 151 HIS 0.003 0.001 HIS B 134 PHE 0.031 0.001 PHE A1197 TYR 0.019 0.001 TYR A1348 ARG 0.007 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 7) link_NAG-ASN : angle 2.00811 ( 21) link_BETA1-4 : bond 0.00142 ( 2) link_BETA1-4 : angle 4.00741 ( 6) hydrogen bonds : bond 0.04208 ( 746) hydrogen bonds : angle 4.77546 ( 2145) SS BOND : bond 0.00578 ( 9) SS BOND : angle 0.82214 ( 18) covalent geometry : bond 0.00305 (11965) covalent geometry : angle 0.62762 (16214) *********************** 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 276 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 219 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 222 LEU cc_start: 0.8241 (mt) cc_final: 0.7996 (mt) REVERT: A 300 ARG cc_start: 0.7386 (ttm-80) cc_final: 0.7003 (mtt-85) REVERT: A 301 LYS cc_start: 0.7575 (mtmt) cc_final: 0.7198 (mmtt) REVERT: A 742 MET cc_start: 0.3608 (mmt) cc_final: 0.2438 (mtt) REVERT: A 798 MET cc_start: 0.4033 (ptm) cc_final: 0.3653 (ptm) REVERT: A 820 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7152 (mm) REVERT: A 843 PHE cc_start: 0.5062 (OUTLIER) cc_final: 0.4842 (m-80) REVERT: A 890 LYS cc_start: 0.7460 (mtpp) cc_final: 0.7219 (mmtt) REVERT: A 969 SER cc_start: 0.5763 (OUTLIER) cc_final: 0.5463 (m) REVERT: A 1254 PHE cc_start: 0.7335 (m-10) cc_final: 0.6984 (m-80) REVERT: A 1287 LYS cc_start: 0.8306 (tppt) cc_final: 0.7710 (mtpp) REVERT: A 1305 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7069 (tt0) REVERT: A 1309 VAL cc_start: 0.7981 (p) cc_final: 0.7722 (m) REVERT: A 1349 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: A 1435 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7274 (pt) REVERT: A 1447 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7362 (t80) REVERT: A 1541 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7936 (tp-100) REVERT: A 1610 ARG cc_start: 0.6333 (mtp85) cc_final: 0.6125 (mtp180) REVERT: A 1663 MET cc_start: 0.8880 (mtp) cc_final: 0.8639 (mtp) REVERT: A 1727 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: B 69 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8239 (ttpt) REVERT: B 99 LYS cc_start: 0.7168 (tptm) cc_final: 0.6809 (tppt) REVERT: B 154 MET cc_start: 0.6595 (mtt) cc_final: 0.6200 (mtm) REVERT: B 160 GLU cc_start: 0.7425 (tt0) cc_final: 0.7088 (tt0) REVERT: B 162 MET cc_start: 0.6456 (tpt) cc_final: 0.6219 (tpt) REVERT: B 182 TYR cc_start: 0.7749 (t80) cc_final: 0.7367 (t80) outliers start: 57 outliers final: 36 residues processed: 260 average time/residue: 0.2245 time to fit residues: 84.2387 Evaluate side-chains 255 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 164 THR 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 326 GLU Chi-restraints excluded: chain A residue 348 SER 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 817 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 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 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 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 1485 MET Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 66 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 104 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4542 r_free = 0.4542 target = 0.225618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.176939 restraints weight = 12573.198| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.74 r_work: 0.3681 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11983 Z= 0.131 Angle : 0.627 10.979 16259 Z= 0.316 Chirality : 0.042 0.294 1886 Planarity : 0.003 0.040 1978 Dihedral : 6.077 58.273 1760 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.14 % Allowed : 25.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1419 helix: 0.70 (0.17), residues: 861 sheet: -0.53 (0.46), residues: 126 loop : -1.74 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 151 HIS 0.003 0.000 HIS B 134 PHE 0.014 0.001 PHE A1740 TYR 0.019 0.001 TYR A1348 ARG 0.007 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 7) link_NAG-ASN : angle 2.85658 ( 21) link_BETA1-4 : bond 0.00088 ( 2) link_BETA1-4 : angle 3.68957 ( 6) hydrogen bonds : bond 0.04095 ( 746) hydrogen bonds : angle 4.73867 ( 2145) SS BOND : bond 0.00499 ( 9) SS BOND : angle 0.96262 ( 18) covalent geometry : bond 0.00278 (11965) covalent geometry : angle 0.61401 (16214) *********************** 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 272 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8543 (mp) REVERT: A 164 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 222 LEU cc_start: 0.8211 (mt) cc_final: 0.7918 (mt) REVERT: A 291 ASN cc_start: 0.7279 (p0) cc_final: 0.7044 (p0) REVERT: A 300 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.6860 (mtt-85) REVERT: A 301 LYS cc_start: 0.7481 (mtmt) cc_final: 0.7050 (mmtt) REVERT: A 742 MET cc_start: 0.3641 (mmt) cc_final: 0.2502 (mtt) REVERT: A 798 MET cc_start: 0.4085 (ptm) cc_final: 0.3660 (ptm) REVERT: A 820 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7251 (mm) REVERT: A 890 LYS cc_start: 0.7376 (mtpp) cc_final: 0.7116 (mmtt) REVERT: A 912 ASP cc_start: 0.8605 (m-30) cc_final: 0.8080 (m-30) REVERT: A 969 SER cc_start: 0.5640 (OUTLIER) cc_final: 0.5387 (m) REVERT: A 1254 PHE cc_start: 0.7371 (m-10) cc_final: 0.7011 (m-80) REVERT: A 1287 LYS cc_start: 0.8317 (tppt) cc_final: 0.7763 (mtpp) REVERT: A 1305 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7005 (tt0) REVERT: A 1309 VAL cc_start: 0.7811 (p) cc_final: 0.7571 (m) REVERT: A 1349 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6803 (pt0) REVERT: A 1435 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7261 (pt) REVERT: A 1447 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7349 (t80) REVERT: A 1540 SER cc_start: 0.7514 (t) cc_final: 0.7280 (m) REVERT: A 1663 MET cc_start: 0.8891 (mtp) cc_final: 0.8642 (mtp) REVERT: A 1714 ASP cc_start: 0.6953 (m-30) cc_final: 0.6732 (m-30) REVERT: A 1727 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: B 69 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8204 (ttpt) REVERT: B 99 LYS cc_start: 0.7111 (tptm) cc_final: 0.6688 (tppt) REVERT: B 152 ARG cc_start: 0.8012 (ptm160) cc_final: 0.7766 (ptm-80) REVERT: B 154 MET cc_start: 0.6605 (mtt) cc_final: 0.6265 (mtm) REVERT: B 160 GLU cc_start: 0.7351 (tt0) cc_final: 0.6995 (tt0) REVERT: B 162 MET cc_start: 0.6372 (tpt) cc_final: 0.6163 (tpt) REVERT: B 182 TYR cc_start: 0.7714 (t80) cc_final: 0.7412 (t80) outliers start: 53 outliers final: 34 residues processed: 257 average time/residue: 0.2280 time to fit residues: 85.2189 Evaluate side-chains 256 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 164 THR 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 348 SER 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 820 LEU Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 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 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 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 1485 MET Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1672 GLU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 127 optimal weight: 0.0770 chunk 40 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.225791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177615 restraints weight = 12494.073| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.22 r_work: 0.3689 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11983 Z= 0.133 Angle : 0.639 12.727 16259 Z= 0.324 Chirality : 0.043 0.294 1886 Planarity : 0.004 0.039 1978 Dihedral : 6.032 58.083 1760 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.67 % Allowed : 25.96 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1419 helix: 0.80 (0.17), residues: 861 sheet: -0.42 (0.46), residues: 126 loop : -1.72 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 151 HIS 0.002 0.000 HIS B 134 PHE 0.037 0.001 PHE A1197 TYR 0.019 0.001 TYR A1348 ARG 0.007 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 7) link_NAG-ASN : angle 2.71456 ( 21) link_BETA1-4 : bond 0.00123 ( 2) link_BETA1-4 : angle 3.43576 ( 6) hydrogen bonds : bond 0.04060 ( 746) hydrogen bonds : angle 4.72227 ( 2145) SS BOND : bond 0.00847 ( 9) SS BOND : angle 2.15556 ( 18) covalent geometry : bond 0.00283 (11965) covalent geometry : angle 0.62521 (16214) *********************** 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 262 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8822 (mt) cc_final: 0.8523 (mp) REVERT: A 164 THR cc_start: 0.8663 (t) cc_final: 0.8374 (p) REVERT: A 291 ASN cc_start: 0.7176 (p0) cc_final: 0.6950 (p0) REVERT: A 300 ARG cc_start: 0.7241 (ttm-80) cc_final: 0.6815 (mtt-85) REVERT: A 301 LYS cc_start: 0.7468 (mtmt) cc_final: 0.7037 (mmtt) REVERT: A 742 MET cc_start: 0.3609 (mmt) cc_final: 0.2447 (mtt) REVERT: A 798 MET cc_start: 0.3976 (ptm) cc_final: 0.3577 (ptm) REVERT: A 820 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7267 (mm) REVERT: A 912 ASP cc_start: 0.8551 (m-30) cc_final: 0.8033 (m-30) REVERT: A 969 SER cc_start: 0.5693 (OUTLIER) cc_final: 0.5477 (m) REVERT: A 1254 PHE cc_start: 0.7315 (m-10) cc_final: 0.6942 (m-80) REVERT: A 1287 LYS cc_start: 0.8297 (tppt) cc_final: 0.7735 (mtpp) REVERT: A 1305 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: A 1349 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.6838 (pt0) REVERT: A 1435 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7270 (pt) REVERT: A 1540 SER cc_start: 0.7516 (t) cc_final: 0.7281 (m) REVERT: A 1665 ASN cc_start: 0.7809 (m-40) cc_final: 0.6662 (m-40) REVERT: A 1714 ASP cc_start: 0.6890 (m-30) cc_final: 0.6660 (m-30) REVERT: A 1727 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: A 1741 VAL cc_start: 0.8632 (t) cc_final: 0.8426 (t) REVERT: B 99 LYS cc_start: 0.7050 (tptm) cc_final: 0.6692 (tppt) REVERT: B 160 GLU cc_start: 0.7268 (tt0) cc_final: 0.6886 (tt0) REVERT: B 162 MET cc_start: 0.6444 (tpt) cc_final: 0.6190 (tpt) REVERT: B 182 TYR cc_start: 0.7665 (t80) cc_final: 0.7378 (t80) outliers start: 47 outliers final: 32 residues processed: 247 average time/residue: 0.2238 time to fit residues: 80.4166 Evaluate side-chains 246 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 247 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 364 GLU 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 820 LEU Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 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 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 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 1485 MET Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 40.0000 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4538 r_free = 0.4538 target = 0.225033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.176453 restraints weight = 12572.467| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.57 r_work: 0.3659 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11983 Z= 0.143 Angle : 0.650 12.019 16259 Z= 0.328 Chirality : 0.043 0.289 1886 Planarity : 0.004 0.036 1978 Dihedral : 5.995 59.970 1758 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.60 % Allowed : 25.96 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1419 helix: 0.87 (0.17), residues: 857 sheet: -0.39 (0.46), residues: 126 loop : -1.64 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 151 HIS 0.002 0.000 HIS A 766 PHE 0.025 0.001 PHE A1197 TYR 0.020 0.001 TYR A1348 ARG 0.008 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 7) link_NAG-ASN : angle 3.31433 ( 21) link_BETA1-4 : bond 0.00068 ( 2) link_BETA1-4 : angle 3.30993 ( 6) hydrogen bonds : bond 0.04118 ( 746) hydrogen bonds : angle 4.75882 ( 2145) SS BOND : bond 0.00756 ( 9) SS BOND : angle 1.94029 ( 18) covalent geometry : bond 0.00316 (11965) covalent geometry : angle 0.63337 (16214) *********************** 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 258 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8528 (mp) REVERT: A 164 THR cc_start: 0.8674 (t) cc_final: 0.8404 (p) REVERT: A 214 ARG cc_start: 0.6365 (ttt90) cc_final: 0.6162 (ttt-90) REVERT: A 301 LYS cc_start: 0.7524 (mtmt) cc_final: 0.7022 (mmtt) REVERT: A 742 MET cc_start: 0.3711 (mmt) cc_final: 0.2570 (mtt) REVERT: A 798 MET cc_start: 0.4044 (ptm) cc_final: 0.3631 (ptm) REVERT: A 820 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7222 (mm) REVERT: A 912 ASP cc_start: 0.8617 (m-30) cc_final: 0.8105 (m-30) REVERT: A 969 SER cc_start: 0.5703 (OUTLIER) cc_final: 0.5485 (m) REVERT: A 1254 PHE cc_start: 0.7272 (m-10) cc_final: 0.6888 (m-80) REVERT: A 1305 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: A 1349 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: A 1435 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7308 (pt) REVERT: A 1447 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7383 (t80) REVERT: A 1540 SER cc_start: 0.7534 (t) cc_final: 0.7303 (m) REVERT: A 1714 ASP cc_start: 0.7012 (m-30) cc_final: 0.6715 (m-30) REVERT: A 1727 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: B 72 ARG cc_start: 0.7358 (ttt90) cc_final: 0.7096 (ttt-90) REVERT: B 87 GLU cc_start: 0.7499 (tt0) cc_final: 0.7235 (mt-10) REVERT: B 99 LYS cc_start: 0.7110 (tptm) cc_final: 0.6748 (tppt) REVERT: B 152 ARG cc_start: 0.8171 (ptm160) cc_final: 0.7887 (ptm-80) REVERT: B 160 GLU cc_start: 0.7284 (tt0) cc_final: 0.6862 (tt0) REVERT: B 162 MET cc_start: 0.6470 (tpt) cc_final: 0.6216 (tpt) REVERT: B 182 TYR cc_start: 0.7709 (t80) cc_final: 0.7406 (t80) outliers start: 46 outliers final: 32 residues processed: 244 average time/residue: 0.2343 time to fit residues: 82.9327 Evaluate side-chains 246 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 311 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 413 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 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 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 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 1485 MET Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 59 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4542 r_free = 0.4542 target = 0.225474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.177508 restraints weight = 12337.515| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 3.32 r_work: 0.3694 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11983 Z= 0.144 Angle : 0.716 25.296 16259 Z= 0.344 Chirality : 0.046 0.691 1886 Planarity : 0.004 0.038 1978 Dihedral : 6.298 59.623 1756 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.60 % Allowed : 26.11 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1419 helix: 0.89 (0.17), residues: 857 sheet: -0.35 (0.46), residues: 126 loop : -1.60 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 151 HIS 0.002 0.000 HIS A 766 PHE 0.028 0.001 PHE A1197 TYR 0.020 0.001 TYR A1348 ARG 0.009 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 7) link_NAG-ASN : angle 7.59101 ( 21) link_BETA1-4 : bond 0.00140 ( 2) link_BETA1-4 : angle 3.19057 ( 6) hydrogen bonds : bond 0.04092 ( 746) hydrogen bonds : angle 4.71898 ( 2145) SS BOND : bond 0.00691 ( 9) SS BOND : angle 1.70577 ( 18) covalent geometry : bond 0.00315 (11965) covalent geometry : angle 0.65740 (16214) ********************** 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 256 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8490 (mp) REVERT: A 164 THR cc_start: 0.8641 (t) cc_final: 0.8391 (p) REVERT: A 166 GLU cc_start: 0.8110 (tt0) cc_final: 0.7744 (mt-10) REVERT: A 301 LYS cc_start: 0.7515 (mtmt) cc_final: 0.7000 (mmtt) REVERT: A 742 MET cc_start: 0.3661 (mmt) cc_final: 0.2496 (mtp) REVERT: A 798 MET cc_start: 0.4017 (ptm) cc_final: 0.3642 (ptm) REVERT: A 912 ASP cc_start: 0.8557 (m-30) cc_final: 0.8029 (m-30) REVERT: A 969 SER cc_start: 0.5693 (OUTLIER) cc_final: 0.5481 (m) REVERT: A 1254 PHE cc_start: 0.7222 (m-10) cc_final: 0.6843 (m-80) REVERT: A 1305 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: A 1349 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: A 1435 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7245 (pt) REVERT: A 1447 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7336 (t80) REVERT: A 1540 SER cc_start: 0.7539 (t) cc_final: 0.7311 (m) REVERT: A 1714 ASP cc_start: 0.7133 (m-30) cc_final: 0.6881 (m-30) REVERT: A 1727 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: B 72 ARG cc_start: 0.7321 (ttt90) cc_final: 0.7113 (ttt-90) REVERT: B 87 GLU cc_start: 0.7467 (tt0) cc_final: 0.7204 (mt-10) REVERT: B 99 LYS cc_start: 0.7048 (tptm) cc_final: 0.6706 (tppt) REVERT: B 160 GLU cc_start: 0.7245 (tt0) cc_final: 0.6896 (tt0) REVERT: B 162 MET cc_start: 0.6437 (tpt) cc_final: 0.6212 (tpt) REVERT: B 182 TYR cc_start: 0.7712 (t80) cc_final: 0.7421 (t80) outliers start: 46 outliers final: 34 residues processed: 242 average time/residue: 0.2346 time to fit residues: 83.3030 Evaluate side-chains 247 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 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 925 CYS 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 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 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 1485 MET Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4549 r_free = 0.4549 target = 0.226309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.179612 restraints weight = 12411.655| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.75 r_work: 0.3705 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11983 Z= 0.136 Angle : 0.675 24.768 16259 Z= 0.332 Chirality : 0.045 0.543 1886 Planarity : 0.004 0.040 1978 Dihedral : 6.093 57.858 1756 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.28 % Allowed : 26.35 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1419 helix: 0.92 (0.17), residues: 859 sheet: -0.32 (0.47), residues: 126 loop : -1.54 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 151 HIS 0.002 0.000 HIS A 766 PHE 0.025 0.001 PHE A1197 TYR 0.018 0.001 TYR A1348 ARG 0.009 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.01040 ( 7) link_NAG-ASN : angle 6.51660 ( 21) link_BETA1-4 : bond 0.00127 ( 2) link_BETA1-4 : angle 2.99945 ( 6) hydrogen bonds : bond 0.04059 ( 746) hydrogen bonds : angle 4.70218 ( 2145) SS BOND : bond 0.00613 ( 9) SS BOND : angle 1.50585 ( 18) covalent geometry : bond 0.00295 (11965) covalent geometry : angle 0.62888 (16214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7649.58 seconds wall clock time: 134 minutes 15.31 seconds (8055.31 seconds total)