Starting phenix.real_space_refine on Fri Mar 14 00:56:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dur_30867/03_2025/7dur_30867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dur_30867/03_2025/7dur_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_30867/03_2025/7dur_30867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dur_30867/03_2025/7dur_30867.map" model { file = "/net/cci-nas-00/data/ceres_data/7dur_30867/03_2025/7dur_30867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dur_30867/03_2025/7dur_30867.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 8.29, per 1000 atoms: 0.90 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.98 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: 2.91 Time building geometry restraints manager: 2.99 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: 5168 17.88 - 35.75: 517 35.75 - 53.63: 131 53.63 - 71.50: 42 71.50 - 89.38: 8 Dihedral angle restraints: 5866 sinusoidal: 2581 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 5863 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: 1.320 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 27.220 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 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 9434 Z= 0.496 Angle : 1.094 11.361 12823 Z= 0.593 Chirality : 0.066 0.476 1426 Planarity : 0.007 0.055 1593 Dihedral : 15.688 89.376 3722 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (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 TRP 0.038 0.004 TRP R 87 HIS 0.011 0.002 HIS B 142 PHE 0.053 0.004 PHE R 280 TYR 0.034 0.004 TYR B 264 ARG 0.006 0.001 ARG B 68 *********************** 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 : 1.129 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 331 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8891 (p0) REVERT: B 217 MET cc_start: 0.6367 (ptt) cc_final: 0.5314 (ptt) REVERT: B 264 TYR cc_start: 0.5898 (m-80) cc_final: 0.4706 (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: 0.6438 (m-80) REVERT: N 81 LEU cc_start: 0.8637 (tp) cc_final: 0.8373 (pp) REVERT: R 48 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5159 (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: 0.8378 (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: 0.8047 (mmp-170) outliers start: 45 outliers final: 15 residues processed: 284 average time/residue: 0.2554 time to fit residues: 94.9849 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 38 LYS Chi-restraints excluded: chain R residue 39 TRP 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 92 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** 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 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 = 0.4324 r_free = 0.4324 target = 0.095621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.074398 restraints weight = 43173.401| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 7.55 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9434 Z= 0.256 Angle : 0.740 7.831 12823 Z= 0.387 Chirality : 0.046 0.170 1426 Planarity : 0.005 0.043 1593 Dihedral : 9.449 77.575 1672 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.92 % Allowed : 15.68 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1104 helix: -0.28 (0.24), residues: 427 sheet: -0.85 (0.31), residues: 220 loop : -1.06 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 36 HIS 0.008 0.001 HIS B 225 PHE 0.031 0.002 PHE N 29 TYR 0.039 0.002 TYR N 32 ARG 0.007 0.001 ARG A 347 *********************** 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 202 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 1.039 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: A 60 MET cc_start: 0.8173 (mmm) cc_final: 0.7969 (mmm) REVERT: B 59 TYR cc_start: 0.7450 (m-80) cc_final: 0.6982 (m-80) REVERT: B 61 MET cc_start: 0.7802 (ppp) cc_final: 0.7552 (ppp) REVERT: B 75 GLN cc_start: 0.9028 (mm110) cc_final: 0.8254 (mm110) REVERT: B 117 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8522 (mm) REVERT: B 188 MET cc_start: 0.8308 (mmp) cc_final: 0.7260 (mmp) REVERT: B 264 TYR cc_start: 0.8152 (m-80) cc_final: 0.7750 (m-80) REVERT: B 296 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8074 (m) REVERT: G 21 MET cc_start: 0.4786 (tmm) cc_final: 0.4493 (ttp) REVERT: G 38 MET cc_start: 0.7944 (ptt) cc_final: 0.7578 (ptm) REVERT: N 80 TYR cc_start: 0.8031 (m-80) cc_final: 0.7548 (m-80) REVERT: N 83 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.9113 (mmp) REVERT: R 221 GLN cc_start: 0.9337 (mm110) cc_final: 0.8684 (pp30) REVERT: R 269 TYR cc_start: 0.8948 (m-80) cc_final: 0.8000 (m-80) REVERT: R 353 THR cc_start: 0.9697 (m) cc_final: 0.9408 (p) REVERT: R 357 ILE cc_start: 0.9571 (mm) cc_final: 0.9320 (mm) REVERT: R 393 PHE cc_start: 0.9093 (m-80) cc_final: 0.8603 (m-10) REVERT: R 397 MET cc_start: 0.9250 (mtm) cc_final: 0.8773 (ptm) REVERT: R 418 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8779 (mm-30) REVERT: R 421 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8567 (mmm160) outliers start: 48 outliers final: 28 residues processed: 187 average time/residue: 0.2155 time to fit residues: 55.7150 Evaluate side-chains 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 37 GLN Chi-restraints excluded: chain R residue 38 LYS 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 78 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 6 optimal weight: 0.1980 chunk 69 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** A 357 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.094301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.073256 restraints weight = 43694.248| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 7.55 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9434 Z= 0.225 Angle : 0.682 11.384 12823 Z= 0.351 Chirality : 0.044 0.185 1426 Planarity : 0.004 0.038 1593 Dihedral : 8.151 70.439 1645 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.51 % Allowed : 18.65 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1104 helix: 0.20 (0.24), residues: 436 sheet: -0.59 (0.34), residues: 205 loop : -0.85 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 36 HIS 0.007 0.001 HIS A 220 PHE 0.019 0.002 PHE R 280 TYR 0.020 0.002 TYR R 148 ARG 0.012 0.001 ARG B 214 *********************** 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 185 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 1.074 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 219 PHE cc_start: 0.8819 (m-80) cc_final: 0.8257 (m-80) REVERT: B 55 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8455 (mt) REVERT: B 59 TYR cc_start: 0.7394 (m-80) cc_final: 0.6774 (m-80) REVERT: B 188 MET cc_start: 0.8377 (mmp) cc_final: 0.7403 (mmp) REVERT: B 296 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8323 (m) REVERT: B 304 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7801 (ppt170) REVERT: G 38 MET cc_start: 0.8093 (ptt) cc_final: 0.7721 (ptm) REVERT: N 80 TYR cc_start: 0.7900 (m-80) cc_final: 0.7080 (m-80) REVERT: N 103 PHE cc_start: 0.8886 (m-10) cc_final: 0.8600 (m-10) REVERT: R 269 TYR cc_start: 0.8949 (m-80) cc_final: 0.8162 (m-80) REVERT: R 357 ILE cc_start: 0.9593 (mm) cc_final: 0.9346 (mm) REVERT: R 393 PHE cc_start: 0.9034 (m-80) cc_final: 0.8538 (m-80) REVERT: R 397 MET cc_start: 0.9229 (mtm) cc_final: 0.8736 (ptm) REVERT: R 421 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8447 (mmm160) outliers start: 44 outliers final: 29 residues processed: 172 average time/residue: 0.2101 time to fit residues: 50.4735 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 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 R residue 31 SER Chi-restraints excluded: chain R residue 33 TRP 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** 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 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.087365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.066580 restraints weight = 44879.335| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 7.21 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 9434 Z= 0.462 Angle : 0.800 10.968 12823 Z= 0.416 Chirality : 0.047 0.179 1426 Planarity : 0.005 0.045 1593 Dihedral : 7.870 62.669 1635 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.94 % Allowed : 20.80 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1104 helix: 0.13 (0.23), residues: 438 sheet: -0.48 (0.35), residues: 212 loop : -1.05 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP R 214 HIS 0.022 0.002 HIS A 220 PHE 0.018 0.003 PHE R 280 TYR 0.024 0.003 TYR R 148 ARG 0.006 0.001 ARG A 42 *********************** 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: 58 poor density : 122 time to evaluate : 0.955 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: 0.8145 (m90) cc_final: 0.7896 (m90) REVERT: B 59 TYR cc_start: 0.7895 (m-80) cc_final: 0.7348 (m-80) REVERT: B 105 TYR cc_start: 0.7903 (t80) cc_final: 0.7531 (t80) REVERT: B 264 TYR cc_start: 0.8311 (m-80) cc_final: 0.7849 (m-80) REVERT: B 296 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8616 (m) REVERT: B 304 ARG cc_start: 0.8459 (mtp180) cc_final: 0.8070 (pmt-80) REVERT: B 325 MET cc_start: 0.8338 (mmm) cc_final: 0.8060 (mmm) REVERT: G 38 MET cc_start: 0.7897 (ptt) cc_final: 0.7571 (ptm) REVERT: N 38 ARG cc_start: 0.8921 (ptm-80) cc_final: 0.8523 (ptm-80) REVERT: N 76 LYS cc_start: 0.8277 (pttp) cc_final: 0.7753 (pttp) REVERT: N 80 TYR cc_start: 0.7968 (m-80) cc_final: 0.7511 (m-80) REVERT: R 233 MET cc_start: 0.8697 (mmm) cc_final: 0.8471 (mmm) REVERT: R 269 TYR cc_start: 0.9058 (m-80) cc_final: 0.8204 (m-80) REVERT: R 357 ILE cc_start: 0.9629 (mm) cc_final: 0.9376 (mm) REVERT: R 393 PHE cc_start: 0.9138 (m-80) cc_final: 0.8651 (m-10) REVERT: R 397 MET cc_start: 0.9267 (mtm) cc_final: 0.8792 (ptp) outliers start: 58 outliers final: 42 residues processed: 164 average time/residue: 0.1984 time to fit residues: 46.2504 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP 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 336 LEU 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 61 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR 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 309 ILE Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 394 GLN 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 78 optimal weight: 3.9990 chunk 16 optimal weight: 0.0570 chunk 84 optimal weight: 0.0670 chunk 5 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 267 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 37 GLN R 171 HIS ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.092919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.071975 restraints weight = 43670.235| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 7.44 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9434 Z= 0.184 Angle : 0.668 12.773 12823 Z= 0.339 Chirality : 0.044 0.303 1426 Planarity : 0.004 0.036 1593 Dihedral : 7.279 58.764 1632 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.41 % Allowed : 22.75 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1104 helix: 0.49 (0.24), residues: 438 sheet: -0.40 (0.35), residues: 202 loop : -0.68 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 36 HIS 0.007 0.001 HIS A 357 PHE 0.021 0.001 PHE R 230 TYR 0.016 0.002 TYR R 42 ARG 0.008 0.001 ARG A 283 *********************** 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 190 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.922 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: 0.8070 (m90) cc_final: 0.7837 (m-70) REVERT: A 219 PHE cc_start: 0.8988 (m-80) cc_final: 0.8431 (m-10) REVERT: A 279 ASN cc_start: 0.9634 (t0) cc_final: 0.9292 (t0) REVERT: A 388 LEU cc_start: 0.9208 (mm) cc_final: 0.8873 (mp) REVERT: B 59 TYR cc_start: 0.7588 (m-80) cc_final: 0.6931 (m-80) REVERT: B 188 MET cc_start: 0.8129 (mmp) cc_final: 0.7656 (mmp) REVERT: B 296 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8352 (m) REVERT: B 304 ARG cc_start: 0.8295 (mtp180) cc_final: 0.7805 (ppt170) REVERT: G 38 MET cc_start: 0.7872 (ptt) cc_final: 0.7518 (ptm) REVERT: N 38 ARG cc_start: 0.8534 (ptm-80) cc_final: 0.8262 (ptm-80) REVERT: N 76 LYS cc_start: 0.8279 (pttp) cc_final: 0.7865 (pttp) REVERT: N 80 TYR cc_start: 0.8014 (m-80) cc_final: 0.7512 (m-80) REVERT: R 221 GLN cc_start: 0.9344 (mm110) cc_final: 0.8722 (pp30) REVERT: R 269 TYR cc_start: 0.9006 (m-80) cc_final: 0.8244 (m-80) REVERT: R 357 ILE cc_start: 0.9602 (mm) cc_final: 0.9350 (mm) REVERT: R 393 PHE cc_start: 0.8998 (m-80) cc_final: 0.8458 (m-80) REVERT: R 397 MET cc_start: 0.9251 (mtm) cc_final: 0.8829 (ptp) REVERT: R 421 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8260 (mmm160) outliers start: 43 outliers final: 29 residues processed: 179 average time/residue: 0.2023 time to fit residues: 51.6145 Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 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 61 THR Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 81 VAL 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 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 82 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 GLN ** 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 = 0.4270 r_free = 0.4270 target = 0.091773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.071218 restraints weight = 42370.736| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 7.21 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9434 Z= 0.210 Angle : 0.663 11.589 12823 Z= 0.335 Chirality : 0.044 0.139 1426 Planarity : 0.004 0.033 1593 Dihedral : 6.798 57.980 1631 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.02 % Allowed : 24.39 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1104 helix: 0.81 (0.24), residues: 434 sheet: -0.27 (0.35), residues: 205 loop : -0.62 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP N 36 HIS 0.007 0.001 HIS A 357 PHE 0.024 0.002 PHE R 156 TYR 0.021 0.002 TYR R 42 ARG 0.006 0.000 ARG A 283 *********************** 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 172 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 1.109 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 59 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.6019 (pp30) REVERT: A 219 PHE cc_start: 0.8970 (m-80) cc_final: 0.8428 (m-80) REVERT: A 221 MET cc_start: 0.9044 (tpp) cc_final: 0.8790 (tpp) REVERT: A 279 ASN cc_start: 0.9606 (t0) cc_final: 0.9259 (t0) REVERT: A 388 LEU cc_start: 0.9149 (mm) cc_final: 0.8877 (mp) REVERT: B 59 TYR cc_start: 0.7586 (m-80) cc_final: 0.6934 (m-80) REVERT: B 188 MET cc_start: 0.8043 (mmp) cc_final: 0.7724 (mmp) REVERT: B 296 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8378 (m) REVERT: B 304 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7824 (pmt-80) REVERT: G 38 MET cc_start: 0.7981 (ptt) cc_final: 0.7659 (ptm) REVERT: N 38 ARG cc_start: 0.8604 (ptm-80) cc_final: 0.8334 (ptm-80) REVERT: N 80 TYR cc_start: 0.8023 (m-80) cc_final: 0.7639 (m-80) REVERT: R 221 GLN cc_start: 0.9353 (mm110) cc_final: 0.8686 (pp30) REVERT: R 269 TYR cc_start: 0.9002 (m-80) cc_final: 0.8234 (m-80) REVERT: R 357 ILE cc_start: 0.9611 (mm) cc_final: 0.9368 (mm) REVERT: R 393 PHE cc_start: 0.9005 (m-80) cc_final: 0.8476 (m-80) REVERT: R 397 MET cc_start: 0.9296 (mtm) cc_final: 0.8769 (ptp) outliers start: 49 outliers final: 34 residues processed: 160 average time/residue: 0.2376 time to fit residues: 55.3269 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 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 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 110 VAL Chi-restraints excluded: chain R residue 35 THR 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 180 HIS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 GLN ** 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 = 0.4282 r_free = 0.4282 target = 0.092059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.071139 restraints weight = 44608.758| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 7.53 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9434 Z= 0.210 Angle : 0.654 8.218 12823 Z= 0.330 Chirality : 0.043 0.135 1426 Planarity : 0.004 0.033 1593 Dihedral : 6.242 57.907 1625 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.71 % Allowed : 24.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1104 helix: 0.88 (0.25), residues: 434 sheet: -0.10 (0.35), residues: 199 loop : -0.64 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 277 HIS 0.008 0.001 HIS A 220 PHE 0.018 0.001 PHE R 156 TYR 0.028 0.002 TYR B 264 ARG 0.007 0.000 ARG A 283 *********************** 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 169 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 123 time to evaluate : 1.039 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 59 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.5990 (pp30) REVERT: A 219 PHE cc_start: 0.8922 (m-80) cc_final: 0.8378 (m-80) REVERT: A 279 ASN cc_start: 0.9619 (t0) cc_final: 0.9279 (t0) REVERT: A 386 MET cc_start: 0.8755 (ppp) cc_final: 0.8418 (ppp) REVERT: A 388 LEU cc_start: 0.9138 (mm) cc_final: 0.8858 (mp) REVERT: B 59 TYR cc_start: 0.7596 (m-80) cc_final: 0.6964 (m-80) REVERT: B 188 MET cc_start: 0.7969 (mmp) cc_final: 0.7679 (mmp) REVERT: B 198 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8083 (tp) REVERT: B 262 MET cc_start: 0.7270 (pmm) cc_final: 0.7065 (pmm) REVERT: B 296 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8442 (m) REVERT: B 304 ARG cc_start: 0.8385 (mtp180) cc_final: 0.7943 (ppt170) REVERT: G 38 MET cc_start: 0.7973 (ptt) cc_final: 0.7741 (ptm) REVERT: N 38 ARG cc_start: 0.8589 (ptm-80) cc_final: 0.8312 (ptm-80) REVERT: N 80 TYR cc_start: 0.8034 (m-80) cc_final: 0.7604 (m-80) REVERT: R 221 GLN cc_start: 0.9326 (mm110) cc_final: 0.8635 (pp30) REVERT: R 269 TYR cc_start: 0.9012 (m-80) cc_final: 0.8234 (m-80) REVERT: R 357 ILE cc_start: 0.9601 (mm) cc_final: 0.9359 (mm) REVERT: R 393 PHE cc_start: 0.8993 (m-80) cc_final: 0.8406 (m-80) REVERT: R 397 MET cc_start: 0.9315 (mtm) cc_final: 0.8753 (ptp) REVERT: R 421 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8213 (mmm160) outliers start: 46 outliers final: 34 residues processed: 162 average time/residue: 0.1985 time to fit residues: 46.2377 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 : 0.937 ------------------------------------------------------------------------------- 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 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 110 VAL Chi-restraints excluded: chain R residue 35 THR 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 180 HIS 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 421 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 6.9990 chunk 8 optimal weight: 0.0020 chunk 43 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 40 optimal weight: 0.4980 chunk 70 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 overall best weight: 1.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 GLN ** 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 = 0.4284 r_free = 0.4284 target = 0.091913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.071167 restraints weight = 44131.315| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 7.37 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9434 Z= 0.206 Angle : 0.678 11.832 12823 Z= 0.341 Chirality : 0.044 0.265 1426 Planarity : 0.004 0.033 1593 Dihedral : 6.148 57.922 1625 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.92 % Allowed : 24.28 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1104 helix: 1.06 (0.25), residues: 428 sheet: -0.14 (0.34), residues: 210 loop : -0.51 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 277 HIS 0.011 0.001 HIS A 357 PHE 0.015 0.001 PHE R 156 TYR 0.016 0.002 TYR R 42 ARG 0.006 0.000 ARG A 283 *********************** 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 169 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 121 time to evaluate : 1.045 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 59 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6113 (pp30) REVERT: A 219 PHE cc_start: 0.8896 (m-80) cc_final: 0.8314 (m-80) REVERT: A 279 ASN cc_start: 0.9596 (t0) cc_final: 0.9254 (t0) REVERT: A 386 MET cc_start: 0.8803 (ppp) cc_final: 0.8460 (ppp) REVERT: A 388 LEU cc_start: 0.9122 (mm) cc_final: 0.8847 (mp) REVERT: B 59 TYR cc_start: 0.7710 (m-80) cc_final: 0.7022 (m-80) REVERT: B 188 MET cc_start: 0.7885 (mmp) cc_final: 0.7639 (mmp) REVERT: B 198 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8110 (tp) REVERT: B 296 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8584 (m) REVERT: B 304 ARG cc_start: 0.8402 (mtp180) cc_final: 0.7954 (ppt170) REVERT: B 325 MET cc_start: 0.8122 (mmp) cc_final: 0.7906 (mmp) REVERT: G 38 MET cc_start: 0.8066 (ptt) cc_final: 0.7858 (ptm) REVERT: N 38 ARG cc_start: 0.8556 (ptm-80) cc_final: 0.8287 (ptm-80) REVERT: N 80 TYR cc_start: 0.8071 (m-80) cc_final: 0.7606 (m-80) REVERT: N 123 GLN cc_start: 0.8473 (pp30) cc_final: 0.8180 (tp40) REVERT: R 143 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8168 (t80) REVERT: R 269 TYR cc_start: 0.9008 (m-80) cc_final: 0.8237 (m-80) REVERT: R 357 ILE cc_start: 0.9612 (mm) cc_final: 0.9371 (mm) REVERT: R 393 PHE cc_start: 0.8996 (m-80) cc_final: 0.8319 (m-80) REVERT: R 397 MET cc_start: 0.9303 (mtm) cc_final: 0.8785 (mtm) outliers start: 48 outliers final: 37 residues processed: 161 average time/residue: 0.1998 time to fit residues: 46.8292 Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN 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 61 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 35 THR 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 180 HIS 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 56 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 30.0000 chunk 100 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS ** R 213 GLN ** 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 = 0.4280 r_free = 0.4280 target = 0.092181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.072078 restraints weight = 42965.532| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 7.08 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9434 Z= 0.201 Angle : 0.687 10.844 12823 Z= 0.347 Chirality : 0.044 0.226 1426 Planarity : 0.004 0.033 1593 Dihedral : 6.071 57.880 1625 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.71 % Allowed : 24.90 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1104 helix: 1.13 (0.25), residues: 428 sheet: -0.19 (0.34), residues: 210 loop : -0.51 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP N 36 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE R 156 TYR 0.023 0.002 TYR B 264 ARG 0.004 0.000 ARG A 283 *********************** 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 167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 1.067 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 59 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6094 (pp30) REVERT: A 219 PHE cc_start: 0.8761 (m-80) cc_final: 0.8196 (m-10) REVERT: A 279 ASN cc_start: 0.9593 (t0) cc_final: 0.9267 (t0) REVERT: A 386 MET cc_start: 0.8799 (ppp) cc_final: 0.8461 (ppp) REVERT: A 388 LEU cc_start: 0.9119 (mm) cc_final: 0.8863 (mp) REVERT: B 59 TYR cc_start: 0.7692 (m-80) cc_final: 0.6991 (m-80) REVERT: B 198 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8137 (tp) REVERT: B 296 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8589 (m) REVERT: B 304 ARG cc_start: 0.8430 (mtp180) cc_final: 0.7993 (ppt170) REVERT: N 38 ARG cc_start: 0.8563 (ptm-80) cc_final: 0.8273 (ptm-80) REVERT: N 80 TYR cc_start: 0.7969 (m-80) cc_final: 0.7533 (m-80) REVERT: N 123 GLN cc_start: 0.8441 (pp30) cc_final: 0.8133 (tp40) REVERT: R 143 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7979 (t80) REVERT: R 269 TYR cc_start: 0.8986 (m-80) cc_final: 0.8222 (m-80) REVERT: R 357 ILE cc_start: 0.9609 (mm) cc_final: 0.9371 (mm) REVERT: R 393 PHE cc_start: 0.8939 (m-80) cc_final: 0.8208 (m-80) REVERT: R 397 MET cc_start: 0.9292 (mtm) cc_final: 0.8757 (mtm) outliers start: 46 outliers final: 38 residues processed: 157 average time/residue: 0.1902 time to fit residues: 43.6602 Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 251 SER 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 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 337 LYS 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 110 VAL Chi-restraints excluded: chain R residue 35 THR 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 180 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.0000 chunk 89 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN R 171 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.093417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.073470 restraints weight = 42628.135| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 7.15 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9434 Z= 0.177 Angle : 0.707 10.535 12823 Z= 0.353 Chirality : 0.044 0.217 1426 Planarity : 0.004 0.036 1593 Dihedral : 6.033 58.590 1625 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.59 % Allowed : 26.54 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1104 helix: 1.22 (0.25), residues: 429 sheet: -0.09 (0.34), residues: 208 loop : -0.58 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP N 36 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE R 280 TYR 0.017 0.001 TYR B 105 ARG 0.004 0.000 ARG B 150 ********************** 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 168 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.104 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: A 59 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6094 (pp30) REVERT: A 219 PHE cc_start: 0.8700 (m-80) cc_final: 0.8207 (m-10) REVERT: A 220 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.8265 (t-170) REVERT: A 279 ASN cc_start: 0.9613 (t0) cc_final: 0.9196 (t0) REVERT: A 388 LEU cc_start: 0.9141 (mm) cc_final: 0.8886 (mp) REVERT: B 59 TYR cc_start: 0.7616 (m-80) cc_final: 0.6963 (m-80) REVERT: B 304 ARG cc_start: 0.8447 (mtp180) cc_final: 0.7955 (ppt170) REVERT: N 38 ARG cc_start: 0.8456 (ptm-80) cc_final: 0.8212 (ptm-80) REVERT: N 80 TYR cc_start: 0.7909 (m-80) cc_final: 0.7465 (m-80) REVERT: N 93 VAL cc_start: 0.9319 (t) cc_final: 0.9104 (p) REVERT: N 109 ASP cc_start: 0.4605 (m-30) cc_final: 0.4302 (m-30) REVERT: N 123 GLN cc_start: 0.8434 (pp30) cc_final: 0.8208 (tp40) REVERT: R 269 TYR cc_start: 0.8957 (m-80) cc_final: 0.8207 (m-80) REVERT: R 334 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8325 (tptt) REVERT: R 357 ILE cc_start: 0.9580 (mm) cc_final: 0.9341 (mm) REVERT: R 393 PHE cc_start: 0.8901 (m-80) cc_final: 0.8165 (m-80) REVERT: R 397 MET cc_start: 0.9276 (mtm) cc_final: 0.8725 (mtm) REVERT: R 415 LYS cc_start: 0.9303 (tmtt) cc_final: 0.9027 (ptpp) outliers start: 35 outliers final: 28 residues processed: 160 average time/residue: 0.2010 time to fit residues: 45.9322 Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 276 ILE Chi-restraints excluded: chain A residue 286 SER 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 143 THR Chi-restraints excluded: chain B residue 158 VAL 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 296 VAL Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 180 HIS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 225 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.093307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.073428 restraints weight = 43487.971| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 7.19 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9434 Z= 0.189 Angle : 0.717 11.117 12823 Z= 0.356 Chirality : 0.044 0.211 1426 Planarity : 0.004 0.035 1593 Dihedral : 5.932 58.670 1625 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.59 % Allowed : 26.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1104 helix: 1.22 (0.25), residues: 429 sheet: -0.16 (0.34), residues: 208 loop : -0.56 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 36 HIS 0.014 0.001 HIS B 225 PHE 0.017 0.001 PHE R 280 TYR 0.020 0.002 TYR B 264 ARG 0.004 0.000 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5107.28 seconds wall clock time: 90 minutes 0.65 seconds (5400.65 seconds total)