Starting phenix.real_space_refine on Thu Jul 2 17:06:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dur_30867/07_2026/7dur_30867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dur_30867/07_2026/7dur_30867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dur_30867/07_2026/7dur_30867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dur_30867/07_2026/7dur_30867.map" model { file = "/net/cci-nas-00/data/ceres_data/7dur_30867/07_2026/7dur_30867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dur_30867/07_2026/7dur_30867.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dur_30867/07_2026/7dur_30867.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dur_30867/07_2026/7dur_30867.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 54 5.16 5 Cl 2 4.86 5 C 5920 2.51 5 N 1571 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9211 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1957 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3079 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 14, 'TRANS': 356} Chain breaks: 4 Chain: "R" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 185 Unusual residues: {'CLR': 6, 'HNO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 1.72, per 1000 atoms: 0.19 Number of scatterers: 9211 At special positions: 0 Unit cell: (94.05, 95.095, 156.75, 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) Cl 2 17.00 S 54 16.00 O 1664 8.00 N 1571 7.00 C 5920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.01 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 264.7 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.9% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 11 through 38 removed outlier: 4.262A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.770A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.904A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.834A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 389 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.689A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.911A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 53 removed outlier: 3.663A pdb=" N VAL R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 94 Processing helix chain 'R' and resid 123 through 127 removed outlier: 4.281A pdb=" N CYS R 126 " --> pdb=" O LEU R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 169 removed outlier: 3.810A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 212 removed outlier: 4.007A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 222 Processing helix chain 'R' and resid 223 through 257 removed outlier: 4.200A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 292 removed outlier: 3.604A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.596A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 removed outlier: 3.843A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 368 removed outlier: 4.303A pdb=" N PHE R 367 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 381 through 404 removed outlier: 4.162A pdb=" N THR R 391 " --> pdb=" O GLU R 387 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.006A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.582A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.939A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.859A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.747A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.201A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.945A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.578A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 82 through 84 removed outlier: 3.549A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2886 1.34 - 1.46: 2043 1.46 - 1.58: 4430 1.58 - 1.70: 1 1.70 - 1.82: 74 Bond restraints: 9434 Sorted by residual: bond pdb=" C14 HNO R 701 " pdb=" N15 HNO R 701 " ideal model delta sigma weight residual 1.348 1.458 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" CA GLU A 314 " pdb=" C GLU A 314 " ideal model delta sigma weight residual 1.522 1.447 0.074 1.72e-02 3.38e+03 1.87e+01 bond pdb=" N LEU R 32 " pdb=" CA LEU R 32 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.40e-02 5.10e+03 9.53e+00 bond pdb=" C20 HNO R 701 " pdb=" C21 HNO R 701 " ideal model delta sigma weight residual 1.418 1.359 0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" CA SER R 31 " pdb=" C SER R 31 " ideal model delta sigma weight residual 1.523 1.562 -0.039 1.34e-02 5.57e+03 8.34e+00 ... (remaining 9429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 12196 2.27 - 4.54: 532 4.54 - 6.82: 72 6.82 - 9.09: 17 9.09 - 11.36: 6 Bond angle restraints: 12823 Sorted by residual: angle pdb=" N LEU R 32 " pdb=" CA LEU R 32 " pdb=" C LEU R 32 " ideal model delta sigma weight residual 113.15 103.96 9.19 1.19e+00 7.06e-01 5.97e+01 angle pdb=" N HIS R 212 " pdb=" CA HIS R 212 " pdb=" C HIS R 212 " ideal model delta sigma weight residual 111.74 104.59 7.15 1.35e+00 5.49e-01 2.80e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 117.19 3.05 6.30e-01 2.52e+00 2.34e+01 angle pdb=" CA TRP A 277 " pdb=" CB TRP A 277 " pdb=" CG TRP A 277 " ideal model delta sigma weight residual 113.60 105.95 7.65 1.90e+00 2.77e-01 1.62e+01 angle pdb=" C THR A 263 " pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta sigma weight residual 122.82 128.08 -5.26 1.42e+00 4.96e-01 1.37e+01 ... (remaining 12818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4863 17.88 - 35.75: 502 35.75 - 53.63: 123 53.63 - 71.50: 34 71.50 - 89.38: 8 Dihedral angle restraints: 5530 sinusoidal: 2245 harmonic: 3285 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual 93.00 27.19 65.81 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 151.70 -58.70 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual -86.00 -44.74 -41.26 1 1.00e+01 1.00e-02 2.38e+01 ... (remaining 5527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1267 0.095 - 0.190: 138 0.190 - 0.285: 13 0.285 - 0.381: 6 0.381 - 0.476: 2 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CG LEU R 32 " pdb=" CB LEU R 32 " pdb=" CD1 LEU R 32 " pdb=" CD2 LEU R 32 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" C14 CLR R 703 " pdb=" C13 CLR R 703 " pdb=" C15 CLR R 703 " pdb=" C8 CLR R 703 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C14 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C15 CLR R 702 " pdb=" C8 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 1423 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 372 " 0.023 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ILE A 372 " -0.077 2.00e-02 2.50e+03 pdb=" O ILE A 372 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG A 373 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 410 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLN R 410 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN R 410 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU R 411 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 30 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.89e+00 pdb=" C VAL R 30 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL R 30 " 0.021 2.00e-02 2.50e+03 pdb=" N SER R 31 " 0.018 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 142 2.62 - 3.19: 8414 3.19 - 3.76: 15160 3.76 - 4.33: 21067 4.33 - 4.90: 33311 Nonbonded interactions: 78094 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.048 3.040 nonbonded pdb=" O TRP R 91 " pdb=" OG SER R 94 " model vdw 2.112 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.201 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.219 3.040 nonbonded pdb=" NZ LYS A 271 " pdb=" OD2 ASP N 50 " model vdw 2.242 3.120 ... (remaining 78089 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.940 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 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 : 0.008 0.110 9441 Z= 0.364 Angle : 1.096 11.361 12835 Z= 0.593 Chirality : 0.066 0.476 1426 Planarity : 0.007 0.055 1593 Dihedral : 15.864 89.376 3386 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.61 % Allowed : 7.79 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.23), residues: 1104 helix: -1.79 (0.21), residues: 433 sheet: -1.25 (0.32), residues: 201 loop : -1.46 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 68 TYR 0.034 0.004 TYR B 264 PHE 0.053 0.004 PHE R 280 TRP 0.038 0.004 TRP R 87 HIS 0.011 0.002 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.36 ( 9434) covalent geometry : angle 1.09418 / 0.59 (12823) SS BOND : bond 0.00807 / 0.40 ( 6) SS BOND : angle 2.42541 / 1.49 ( 12) hydrogen bonds : bond 0.09883 / 6.45 ( 458) hydrogen bonds : angle 6.93598 / 4.84 ( 1302) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8890 (p0) REVERT: B 217 MET cc_start: 0.6367 (ptt) cc_final: 0.5633 (ptt) REVERT: B 264 TYR cc_start: 0.5898 (m-80) cc_final: 0.4705 (m-80) REVERT: G 38 MET cc_start: 0.8543 (ptt) cc_final: 0.7896 (ptt) REVERT: N 80 TYR cc_start: 0.6765 (m-80) cc_final: 0.6440 (m-80) REVERT: N 81 LEU cc_start: 0.8637 (tp) cc_final: 0.8374 (pp) REVERT: R 37 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: R 48 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5160 (ptt90) REVERT: R 146 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8743 (tp) REVERT: R 147 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8816 (mt) REVERT: R 203 TRP cc_start: 0.9029 (OUTLIER) cc_final: 0.8599 (t60) REVERT: R 311 LEU cc_start: 0.8624 (tt) cc_final: 0.8379 (mm) REVERT: R 393 PHE cc_start: 0.8781 (m-80) cc_final: 0.8037 (m-10) REVERT: R 410 GLN cc_start: 0.8719 (mt0) cc_final: 0.8484 (mt0) REVERT: R 421 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8080 (mmp-170) outliers start: 45 outliers final: 17 residues processed: 284 average time/residue: 0.0983 time to fit residues: 36.8594 Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 39 TRP Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 43 ARG Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 48 ARG Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 203 TRP Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 412 GLU Chi-restraints excluded: chain R residue 416 SER Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 171 HIS R 180 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.095924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.074668 restraints weight = 43142.577| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 7.59 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9441 Z= 0.179 Angle : 0.748 10.489 12835 Z= 0.387 Chirality : 0.045 0.164 1426 Planarity : 0.005 0.043 1593 Dihedral : 8.935 79.261 1347 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.82 % Allowed : 16.29 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.24), residues: 1104 helix: -0.25 (0.24), residues: 427 sheet: -0.83 (0.32), residues: 215 loop : -1.08 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 347 TYR 0.040 0.002 TYR N 32 PHE 0.032 0.002 PHE N 29 TRP 0.025 0.002 TRP N 36 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 ( 9434) covalent geometry : angle 0.74704 / 0.39 (12823) SS BOND : bond 0.00437 / 0.23 ( 6) SS BOND : angle 1.31161 / 0.70 ( 12) hydrogen bonds : bond 0.04594 / 2.98 ( 458) hydrogen bonds : angle 5.71381 / 4.00 ( 1302) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8129 (mmm) cc_final: 0.7924 (mmm) REVERT: B 59 TYR cc_start: 0.7445 (m-80) cc_final: 0.6958 (m-80) REVERT: B 61 MET cc_start: 0.7814 (ppp) cc_final: 0.7558 (ppp) REVERT: B 75 GLN cc_start: 0.9039 (mm110) cc_final: 0.8253 (mm110) REVERT: B 117 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8533 (mm) REVERT: B 188 MET cc_start: 0.8299 (mmp) cc_final: 0.7220 (mmp) REVERT: B 264 TYR cc_start: 0.8126 (m-80) cc_final: 0.7705 (m-80) REVERT: B 296 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8070 (m) REVERT: G 21 MET cc_start: 0.4739 (tmm) cc_final: 0.4441 (ttp) REVERT: G 38 MET cc_start: 0.7946 (ptt) cc_final: 0.7572 (ptm) REVERT: N 38 ARG cc_start: 0.9072 (ptt180) cc_final: 0.8679 (ptm160) REVERT: N 80 TYR cc_start: 0.8059 (m-80) cc_final: 0.7580 (m-80) REVERT: N 83 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.9157 (mmp) REVERT: R 269 TYR cc_start: 0.8975 (m-80) cc_final: 0.7964 (m-80) REVERT: R 353 THR cc_start: 0.9692 (m) cc_final: 0.9408 (p) REVERT: R 357 ILE cc_start: 0.9573 (mm) cc_final: 0.9322 (mm) REVERT: R 393 PHE cc_start: 0.9092 (m-80) cc_final: 0.8606 (m-10) REVERT: R 397 MET cc_start: 0.9238 (mtm) cc_final: 0.8740 (ptm) REVERT: R 415 LYS cc_start: 0.9149 (ttpp) cc_final: 0.8897 (ptmm) REVERT: R 418 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8680 (mm-30) REVERT: R 421 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8497 (mmm160) outliers start: 47 outliers final: 29 residues processed: 191 average time/residue: 0.0744 time to fit residues: 19.7305 Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 39 TRP Chi-restraints excluded: chain R residue 43 ARG Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.091887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.070984 restraints weight = 44475.543| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 7.51 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9441 Z= 0.214 Angle : 0.707 11.421 12835 Z= 0.368 Chirality : 0.045 0.160 1426 Planarity : 0.005 0.044 1593 Dihedral : 7.085 55.115 1315 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.23 % Allowed : 18.75 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.24), residues: 1104 helix: 0.15 (0.24), residues: 435 sheet: -0.64 (0.34), residues: 217 loop : -0.91 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 214 TYR 0.021 0.002 TYR R 148 PHE 0.020 0.002 PHE R 280 TRP 0.038 0.002 TRP N 36 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 ( 9434) covalent geometry : angle 0.70638 / 0.37 (12823) SS BOND : bond 0.00419 / 0.21 ( 6) SS BOND : angle 0.91096 / 0.45 ( 12) hydrogen bonds : bond 0.04373 / 2.82 ( 458) hydrogen bonds : angle 5.43979 / 3.83 ( 1302) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8591 (mt) REVERT: B 59 TYR cc_start: 0.7550 (m-80) cc_final: 0.7000 (m-80) REVERT: B 188 MET cc_start: 0.8436 (mmp) cc_final: 0.7492 (mmp) REVERT: B 296 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8303 (m) REVERT: G 38 MET cc_start: 0.7928 (ptt) cc_final: 0.7609 (ptm) REVERT: N 38 ARG cc_start: 0.9142 (ptt180) cc_final: 0.8831 (ptm160) REVERT: N 80 TYR cc_start: 0.7828 (m-80) cc_final: 0.7084 (m-80) REVERT: R 269 TYR cc_start: 0.9008 (m-80) cc_final: 0.8175 (m-80) REVERT: R 357 ILE cc_start: 0.9607 (mm) cc_final: 0.9358 (mm) REVERT: R 393 PHE cc_start: 0.9040 (m-80) cc_final: 0.8547 (m-10) REVERT: R 397 MET cc_start: 0.9223 (mtm) cc_final: 0.8756 (ptm) REVERT: R 415 LYS cc_start: 0.9244 (ttpp) cc_final: 0.9027 (ptpt) outliers start: 51 outliers final: 37 residues processed: 165 average time/residue: 0.0816 time to fit residues: 18.9403 Evaluate side-chains 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 0.0070 chunk 13 optimal weight: 8.9990 chunk 84 optimal weight: 0.0070 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 3 GLN R 171 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.092750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.071940 restraints weight = 43696.727| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 7.41 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9441 Z= 0.151 Angle : 0.653 12.878 12835 Z= 0.333 Chirality : 0.043 0.144 1426 Planarity : 0.004 0.035 1593 Dihedral : 6.202 56.519 1303 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.82 % Allowed : 21.21 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.24), residues: 1104 helix: 0.44 (0.24), residues: 434 sheet: -0.44 (0.34), residues: 213 loop : -0.81 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 48 TYR 0.018 0.002 TYR R 148 PHE 0.019 0.002 PHE R 230 TRP 0.021 0.002 TRP N 36 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 9434) covalent geometry : angle 0.65250 / 0.33 (12823) SS BOND : bond 0.00278 / 0.14 ( 6) SS BOND : angle 0.74904 / 0.37 ( 12) hydrogen bonds : bond 0.04073 / 2.64 ( 458) hydrogen bonds : angle 5.20979 / 3.66 ( 1302) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.8012 (m90) cc_final: 0.7769 (m90) REVERT: A 219 PHE cc_start: 0.8863 (m-80) cc_final: 0.8344 (m-80) REVERT: A 323 ASP cc_start: 0.8723 (p0) cc_final: 0.8518 (p0) REVERT: B 55 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8575 (mt) REVERT: B 59 TYR cc_start: 0.7560 (m-80) cc_final: 0.6920 (m-80) REVERT: B 188 MET cc_start: 0.8291 (mmp) cc_final: 0.7530 (mmp) REVERT: B 262 MET cc_start: 0.6006 (ttm) cc_final: 0.5732 (ttt) REVERT: B 296 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8391 (m) REVERT: B 325 MET cc_start: 0.8103 (mmm) cc_final: 0.7852 (mmm) REVERT: G 38 MET cc_start: 0.7862 (ptt) cc_final: 0.7533 (ptm) REVERT: N 76 LYS cc_start: 0.8174 (pttp) cc_final: 0.7736 (pttp) REVERT: N 80 TYR cc_start: 0.7846 (m-80) cc_final: 0.7419 (m-80) REVERT: N 81 LEU cc_start: 0.8857 (pp) cc_final: 0.8555 (pp) REVERT: R 269 TYR cc_start: 0.8987 (m-80) cc_final: 0.8244 (m-80) REVERT: R 357 ILE cc_start: 0.9610 (mm) cc_final: 0.9370 (mm) REVERT: R 393 PHE cc_start: 0.9036 (m-80) cc_final: 0.8538 (m-80) REVERT: R 397 MET cc_start: 0.9210 (mtm) cc_final: 0.8696 (ptm) REVERT: R 421 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8297 (mmm160) outliers start: 47 outliers final: 35 residues processed: 165 average time/residue: 0.0690 time to fit residues: 16.6072 Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 96 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS R 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.092845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.072274 restraints weight = 43710.127| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 7.45 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9441 Z= 0.140 Angle : 0.623 12.338 12835 Z= 0.319 Chirality : 0.042 0.137 1426 Planarity : 0.004 0.034 1593 Dihedral : 5.924 57.973 1300 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.82 % Allowed : 22.13 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1104 helix: 0.62 (0.24), residues: 436 sheet: -0.30 (0.35), residues: 206 loop : -0.67 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 283 TYR 0.026 0.002 TYR R 42 PHE 0.022 0.001 PHE R 156 TRP 0.022 0.002 TRP N 36 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9434) covalent geometry : angle 0.62262 / 0.32 (12823) SS BOND : bond 0.00311 / 0.16 ( 6) SS BOND : angle 0.59205 / 0.31 ( 12) hydrogen bonds : bond 0.03912 / 2.53 ( 458) hydrogen bonds : angle 5.02008 / 3.53 ( 1302) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.8271 (m90) cc_final: 0.8069 (m-70) REVERT: A 219 PHE cc_start: 0.8976 (m-80) cc_final: 0.8422 (m-10) REVERT: A 221 MET cc_start: 0.8772 (tmm) cc_final: 0.8457 (tmm) REVERT: A 323 ASP cc_start: 0.8766 (p0) cc_final: 0.8561 (p0) REVERT: B 55 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8618 (mt) REVERT: B 59 TYR cc_start: 0.7618 (m-80) cc_final: 0.6824 (m-80) REVERT: B 188 MET cc_start: 0.8257 (mmp) cc_final: 0.7554 (mmp) REVERT: B 262 MET cc_start: 0.6173 (ttm) cc_final: 0.5765 (ttt) REVERT: B 296 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8445 (m) REVERT: B 325 MET cc_start: 0.8213 (mmm) cc_final: 0.7985 (mmm) REVERT: G 38 MET cc_start: 0.7891 (ptt) cc_final: 0.7584 (ptm) REVERT: N 80 TYR cc_start: 0.7926 (m-80) cc_final: 0.7669 (m-80) REVERT: R 269 TYR cc_start: 0.9011 (m-80) cc_final: 0.8274 (m-80) REVERT: R 357 ILE cc_start: 0.9618 (mm) cc_final: 0.9381 (mm) REVERT: R 393 PHE cc_start: 0.9046 (m-80) cc_final: 0.8547 (m-80) REVERT: R 397 MET cc_start: 0.9290 (mtm) cc_final: 0.8778 (ptm) REVERT: R 421 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8313 (mmm160) outliers start: 47 outliers final: 32 residues processed: 174 average time/residue: 0.0661 time to fit residues: 16.5321 Evaluate side-chains 154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN R 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.092305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.071806 restraints weight = 43167.369| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 7.31 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9441 Z= 0.150 Angle : 0.652 11.998 12835 Z= 0.328 Chirality : 0.043 0.193 1426 Planarity : 0.004 0.049 1593 Dihedral : 5.390 56.186 1297 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.23 % Allowed : 23.46 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.25), residues: 1104 helix: 0.87 (0.25), residues: 436 sheet: -0.28 (0.35), residues: 206 loop : -0.57 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.026 0.002 TYR R 42 PHE 0.015 0.001 PHE R 280 TRP 0.038 0.002 TRP N 36 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 9434) covalent geometry : angle 0.65230 / 0.33 (12823) SS BOND : bond 0.00344 / 0.18 ( 6) SS BOND : angle 0.67218 / 0.36 ( 12) hydrogen bonds : bond 0.03895 / 2.51 ( 458) hydrogen bonds : angle 4.99889 / 3.50 ( 1302) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8287 (mm-30) REVERT: A 41 HIS cc_start: 0.8230 (m90) cc_final: 0.7836 (m-70) REVERT: A 219 PHE cc_start: 0.8977 (m-80) cc_final: 0.8430 (m-10) REVERT: A 221 MET cc_start: 0.8779 (tmm) cc_final: 0.8306 (tmm) REVERT: A 323 ASP cc_start: 0.8776 (p0) cc_final: 0.8568 (p0) REVERT: B 59 TYR cc_start: 0.7509 (m-80) cc_final: 0.6902 (m-80) REVERT: B 75 GLN cc_start: 0.8913 (mm110) cc_final: 0.8291 (mm110) REVERT: B 188 MET cc_start: 0.8130 (mmp) cc_final: 0.7644 (mmp) REVERT: B 296 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8395 (m) REVERT: G 38 MET cc_start: 0.8023 (ptt) cc_final: 0.7744 (ptm) REVERT: N 80 TYR cc_start: 0.7999 (m-80) cc_final: 0.7604 (m-80) REVERT: R 269 TYR cc_start: 0.9006 (m-80) cc_final: 0.8267 (m-80) REVERT: R 357 ILE cc_start: 0.9616 (mm) cc_final: 0.9382 (mm) REVERT: R 393 PHE cc_start: 0.9026 (m-80) cc_final: 0.8501 (m-80) REVERT: R 397 MET cc_start: 0.9247 (mtm) cc_final: 0.8700 (ptp) REVERT: R 421 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8272 (mmm160) outliers start: 51 outliers final: 38 residues processed: 161 average time/residue: 0.0674 time to fit residues: 15.6517 Evaluate side-chains 154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS R 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.090195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.069139 restraints weight = 44798.694| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 7.54 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9441 Z= 0.208 Angle : 0.688 10.466 12835 Z= 0.351 Chirality : 0.045 0.190 1426 Planarity : 0.004 0.043 1593 Dihedral : 5.548 57.207 1297 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.84 % Allowed : 23.26 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.25), residues: 1104 helix: 0.83 (0.24), residues: 433 sheet: -0.35 (0.35), residues: 217 loop : -0.64 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 283 TYR 0.023 0.002 TYR R 88 PHE 0.015 0.002 PHE R 280 TRP 0.029 0.002 TRP N 36 HIS 0.014 0.002 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 ( 9434) covalent geometry : angle 0.68744 / 0.35 (12823) SS BOND : bond 0.00349 / 0.17 ( 6) SS BOND : angle 0.77895 / 0.43 ( 12) hydrogen bonds : bond 0.04064 / 2.60 ( 458) hydrogen bonds : angle 5.12579 / 3.60 ( 1302) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.8215 (m90) cc_final: 0.7866 (m90) REVERT: A 219 PHE cc_start: 0.8938 (m-80) cc_final: 0.8438 (m-10) REVERT: A 221 MET cc_start: 0.8856 (tmm) cc_final: 0.8431 (tmm) REVERT: B 59 TYR cc_start: 0.7596 (m-80) cc_final: 0.6890 (m-80) REVERT: B 188 MET cc_start: 0.8218 (mmp) cc_final: 0.7750 (mmp) REVERT: B 198 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8019 (tp) REVERT: B 264 TYR cc_start: 0.8732 (m-80) cc_final: 0.8296 (m-80) REVERT: B 296 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8540 (m) REVERT: G 38 MET cc_start: 0.7925 (ptt) cc_final: 0.7656 (ptm) REVERT: N 76 LYS cc_start: 0.8263 (pttp) cc_final: 0.7801 (pttp) REVERT: N 80 TYR cc_start: 0.8015 (m-80) cc_final: 0.7523 (m-80) REVERT: N 81 LEU cc_start: 0.8864 (pp) cc_final: 0.8639 (pt) REVERT: R 243 TRP cc_start: 0.7974 (m100) cc_final: 0.7397 (m100) REVERT: R 269 TYR cc_start: 0.9021 (m-80) cc_final: 0.8201 (m-80) REVERT: R 357 ILE cc_start: 0.9619 (mm) cc_final: 0.9385 (mm) REVERT: R 393 PHE cc_start: 0.9061 (m-80) cc_final: 0.8520 (m-80) REVERT: R 397 MET cc_start: 0.9289 (mtm) cc_final: 0.8744 (ptp) REVERT: R 421 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8259 (mmm160) outliers start: 57 outliers final: 40 residues processed: 160 average time/residue: 0.0678 time to fit residues: 15.9645 Evaluate side-chains 157 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 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 = 0.4291 r_free = 0.4291 target = 0.092183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.071348 restraints weight = 43499.603| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 7.33 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9441 Z= 0.142 Angle : 0.678 11.550 12835 Z= 0.340 Chirality : 0.043 0.146 1426 Planarity : 0.004 0.036 1593 Dihedral : 5.270 59.496 1293 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.41 % Allowed : 24.59 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1104 helix: 1.01 (0.25), residues: 429 sheet: -0.31 (0.35), residues: 211 loop : -0.61 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.035 0.002 TYR B 264 PHE 0.015 0.001 PHE R 156 TRP 0.033 0.002 TRP A 277 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 9434) covalent geometry : angle 0.67762 / 0.34 (12823) SS BOND : bond 0.00190 / 0.09 ( 6) SS BOND : angle 0.66940 / 0.35 ( 12) hydrogen bonds : bond 0.03845 / 2.49 ( 458) hydrogen bonds : angle 5.00647 / 3.51 ( 1302) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.8227 (m90) cc_final: 0.7890 (m90) REVERT: A 219 PHE cc_start: 0.8912 (m-80) cc_final: 0.8375 (m-10) REVERT: A 221 MET cc_start: 0.8846 (tmm) cc_final: 0.8440 (tmm) REVERT: A 386 MET cc_start: 0.8779 (ppp) cc_final: 0.8452 (ppp) REVERT: A 388 LEU cc_start: 0.9158 (mm) cc_final: 0.8914 (mp) REVERT: B 59 TYR cc_start: 0.7527 (m-80) cc_final: 0.6998 (m-80) REVERT: B 75 GLN cc_start: 0.8764 (mm110) cc_final: 0.8239 (mm110) REVERT: B 188 MET cc_start: 0.8038 (mmp) cc_final: 0.7747 (mmp) REVERT: B 198 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8236 (tp) REVERT: B 296 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8581 (m) REVERT: G 38 MET cc_start: 0.8049 (ptt) cc_final: 0.7765 (ptm) REVERT: N 80 TYR cc_start: 0.7959 (m-80) cc_final: 0.7517 (m-80) REVERT: N 93 VAL cc_start: 0.9339 (t) cc_final: 0.8527 (p) REVERT: N 95 TYR cc_start: 0.8776 (m-80) cc_final: 0.8517 (m-80) REVERT: R 243 TRP cc_start: 0.7943 (m100) cc_final: 0.7345 (m100) REVERT: R 269 TYR cc_start: 0.9007 (m-80) cc_final: 0.8221 (m-80) REVERT: R 357 ILE cc_start: 0.9608 (mm) cc_final: 0.9372 (mm) REVERT: R 393 PHE cc_start: 0.8996 (m-80) cc_final: 0.8404 (m-80) REVERT: R 397 MET cc_start: 0.9315 (mtm) cc_final: 0.8743 (ptp) outliers start: 43 outliers final: 32 residues processed: 158 average time/residue: 0.0610 time to fit residues: 14.5672 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS N 53 GLN R 171 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.090190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.069778 restraints weight = 44090.558| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 7.28 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9441 Z= 0.191 Angle : 0.700 9.136 12835 Z= 0.356 Chirality : 0.045 0.273 1426 Planarity : 0.004 0.047 1593 Dihedral : 5.258 56.023 1289 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.12 % Allowed : 24.90 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 1104 helix: 0.91 (0.25), residues: 437 sheet: -0.27 (0.35), residues: 212 loop : -0.74 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 232 TYR 0.027 0.002 TYR R 42 PHE 0.016 0.002 PHE A 222 TRP 0.075 0.003 TRP A 277 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 9434) covalent geometry : angle 0.69993 / 0.36 (12823) SS BOND : bond 0.00371 / 0.19 ( 6) SS BOND : angle 0.79982 / 0.42 ( 12) hydrogen bonds : bond 0.03930 / 2.53 ( 458) hydrogen bonds : angle 5.06494 / 3.55 ( 1302) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.8264 (m90) cc_final: 0.7918 (m90) REVERT: A 219 PHE cc_start: 0.8998 (m-80) cc_final: 0.8499 (m-10) REVERT: A 221 MET cc_start: 0.8805 (tmm) cc_final: 0.8427 (tmm) REVERT: A 386 MET cc_start: 0.8848 (ppp) cc_final: 0.8532 (ppp) REVERT: A 388 LEU cc_start: 0.9147 (mm) cc_final: 0.8871 (mp) REVERT: B 59 TYR cc_start: 0.7646 (m-80) cc_final: 0.7159 (m-80) REVERT: B 75 GLN cc_start: 0.8807 (mm110) cc_final: 0.8494 (mm110) REVERT: B 198 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8167 (tp) REVERT: B 296 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8641 (m) REVERT: G 38 MET cc_start: 0.7945 (ptt) cc_final: 0.7667 (ptm) REVERT: N 80 TYR cc_start: 0.7904 (m-80) cc_final: 0.7457 (m-80) REVERT: R 143 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8113 (t80) REVERT: R 269 TYR cc_start: 0.9045 (m-80) cc_final: 0.8276 (m-80) REVERT: R 357 ILE cc_start: 0.9618 (mm) cc_final: 0.9383 (mm) REVERT: R 393 PHE cc_start: 0.9025 (m-80) cc_final: 0.8388 (m-80) REVERT: R 397 MET cc_start: 0.9294 (mtm) cc_final: 0.8760 (mtm) REVERT: R 415 LYS cc_start: 0.9332 (tmtt) cc_final: 0.9041 (ptpp) outliers start: 50 outliers final: 41 residues processed: 154 average time/residue: 0.0583 time to fit residues: 13.6245 Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 143 PHE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.0050 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS N 53 GLN R 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.092489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.071939 restraints weight = 43737.955| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 7.31 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9441 Z= 0.134 Angle : 0.699 9.977 12835 Z= 0.348 Chirality : 0.044 0.244 1426 Planarity : 0.004 0.040 1593 Dihedral : 5.077 51.887 1289 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.51 % Allowed : 25.00 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.25), residues: 1104 helix: 1.07 (0.25), residues: 430 sheet: -0.25 (0.35), residues: 212 loop : -0.69 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.026 0.002 TYR R 42 PHE 0.015 0.001 PHE R 280 TRP 0.040 0.002 TRP N 36 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9434) covalent geometry : angle 0.69869 / 0.35 (12823) SS BOND : bond 0.00272 / 0.14 ( 6) SS BOND : angle 0.69589 / 0.35 ( 12) hydrogen bonds : bond 0.03746 / 2.43 ( 458) hydrogen bonds : angle 4.94087 / 3.45 ( 1302) Misc. bond : bond 0.00023 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.8268 (m90) cc_final: 0.8039 (m-70) REVERT: A 219 PHE cc_start: 0.8911 (m-80) cc_final: 0.8302 (m-10) REVERT: A 221 MET cc_start: 0.8800 (tmm) cc_final: 0.8504 (tmm) REVERT: A 308 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8898 (mp) REVERT: A 388 LEU cc_start: 0.9192 (mm) cc_final: 0.8914 (mp) REVERT: B 59 TYR cc_start: 0.7557 (m-80) cc_final: 0.7037 (m-80) REVERT: B 75 GLN cc_start: 0.8756 (mm110) cc_final: 0.8357 (mm110) REVERT: B 198 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8219 (tp) REVERT: B 201 SER cc_start: 0.6165 (OUTLIER) cc_final: 0.5513 (p) REVERT: G 38 MET cc_start: 0.7994 (ptt) cc_final: 0.7763 (ptm) REVERT: N 80 TYR cc_start: 0.7898 (m-80) cc_final: 0.7472 (m-80) REVERT: R 143 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8136 (t80) REVERT: R 269 TYR cc_start: 0.9006 (m-80) cc_final: 0.8259 (m-80) REVERT: R 357 ILE cc_start: 0.9609 (mm) cc_final: 0.9369 (mm) REVERT: R 393 PHE cc_start: 0.8977 (m-80) cc_final: 0.8277 (m-80) REVERT: R 397 MET cc_start: 0.9334 (mtm) cc_final: 0.8814 (mtm) REVERT: R 415 LYS cc_start: 0.9326 (tmtt) cc_final: 0.9046 (ptpp) outliers start: 44 outliers final: 33 residues processed: 154 average time/residue: 0.0631 time to fit residues: 14.7304 Evaluate side-chains 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 143 PHE Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 12 optimal weight: 0.0270 chunk 51 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 225 HIS N 53 GLN R 171 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.091095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.070495 restraints weight = 42935.311| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 7.18 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9441 Z= 0.158 Angle : 0.707 9.943 12835 Z= 0.354 Chirality : 0.045 0.241 1426 Planarity : 0.004 0.045 1593 Dihedral : 4.994 45.188 1289 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.10 % Allowed : 26.02 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1104 helix: 1.00 (0.25), residues: 438 sheet: -0.38 (0.34), residues: 221 loop : -0.81 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 232 TYR 0.022 0.002 TYR R 42 PHE 0.021 0.001 PHE A 376 TRP 0.041 0.002 TRP N 36 HIS 0.018 0.002 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 9434) covalent geometry : angle 0.70593 / 0.35 (12823) SS BOND : bond 0.00254 / 0.13 ( 6) SS BOND : angle 1.17810 / 0.55 ( 12) hydrogen bonds : bond 0.03735 / 2.40 ( 458) hydrogen bonds : angle 4.92986 / 3.45 ( 1302) Misc. bond : bond 0.00017 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1975.79 seconds wall clock time: 34 minutes 44.17 seconds (2084.17 seconds total)