Starting phenix.real_space_refine on Sun Jul 27 13:41:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dur_30867/07_2025/7dur_30867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dur_30867/07_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_30867/07_2025/7dur_30867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dur_30867/07_2025/7dur_30867.map" model { file = "/net/cci-nas-00/data/ceres_data/7dur_30867/07_2025/7dur_30867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dur_30867/07_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-5711/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: 5.95, per 1000 atoms: 0.65 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: 2.55 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: 2.74 Time building geometry restraints manager: 3.00 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: 1.110 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.030 Find NCS groups from input model: 0.110 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- 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 9441 Z= 0.364 Angle : 1.096 11.361 12835 Z= 0.593 Chirality : 0.066 0.476 1426 Planarity : 0.007 0.055 1593 Dihedral : 15.688 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 Details of bonding type rmsd hydrogen bonds : bond 0.09883 ( 458) hydrogen bonds : angle 6.93598 ( 1302) SS BOND : bond 0.00807 ( 6) SS BOND : angle 2.42541 ( 12) covalent geometry : bond 0.00765 ( 9434) covalent geometry : angle 1.09418 (12823) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 1.063 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: 0.2585 time to fit residues: 95.8107 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 : 1.032 ------------------------------------------------------------------------------- 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 9441 Z= 0.182 Angle : 0.741 7.831 12835 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 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 458) hydrogen bonds : angle 5.72904 ( 1302) SS BOND : bond 0.00487 ( 6) SS BOND : angle 1.41877 ( 12) covalent geometry : bond 0.00394 ( 9434) covalent geometry : angle 0.73979 (12823) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.945 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: 0.2088 time to fit residues: 53.6902 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 : 0.954 ------------------------------------------------------------------------------- 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: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 264 ASN ** 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 = 0.4312 r_free = 0.4312 target = 0.094714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.073698 restraints weight = 43339.343| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 7.56 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9441 Z= 0.155 Angle : 0.681 11.656 12835 Z= 0.351 Chirality : 0.044 0.185 1426 Planarity : 0.004 0.039 1593 Dihedral : 8.138 69.991 1645 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.51 % Allowed : 18.44 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.24), residues: 1104 helix: 0.21 (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 0.035 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 269 ARG 0.012 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 458) hydrogen bonds : angle 5.31889 ( 1302) SS BOND : bond 0.00496 ( 6) SS BOND : angle 1.03811 ( 12) covalent geometry : bond 0.00334 ( 9434) covalent geometry : angle 0.68091 (12823) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.975 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: 0.8806 (m-80) cc_final: 0.8259 (m-80) REVERT: B 55 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8447 (mt) REVERT: B 59 TYR cc_start: 0.7351 (m-80) cc_final: 0.6912 (m-80) REVERT: B 75 GLN cc_start: 0.8944 (mm110) cc_final: 0.8078 (mm110) REVERT: B 188 MET cc_start: 0.8376 (mmp) cc_final: 0.7392 (mmp) REVERT: B 221 THR cc_start: 0.9338 (m) cc_final: 0.9118 (p) REVERT: B 264 TYR cc_start: 0.8052 (m-80) cc_final: 0.7579 (m-80) REVERT: B 296 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8356 (m) REVERT: G 38 MET cc_start: 0.8093 (ptt) cc_final: 0.7710 (ptm) REVERT: N 80 TYR cc_start: 0.7833 (m-80) cc_final: 0.7039 (m-80) REVERT: N 103 PHE cc_start: 0.8890 (m-10) cc_final: 0.8609 (m-10) REVERT: R 269 TYR cc_start: 0.8958 (m-80) cc_final: 0.8203 (m-80) REVERT: R 357 ILE cc_start: 0.9590 (mm) cc_final: 0.9341 (mm) REVERT: R 393 PHE cc_start: 0.9025 (m-80) cc_final: 0.8525 (m-80) REVERT: R 397 MET cc_start: 0.9219 (mtm) cc_final: 0.8744 (ptm) REVERT: R 415 LYS cc_start: 0.9519 (ptpt) cc_final: 0.9227 (ptpt) REVERT: R 421 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8433 (mmm160) outliers start: 44 outliers final: 29 residues processed: 174 average time/residue: 0.2065 time to fit residues: 50.4855 Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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: 4.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.090537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.069562 restraints weight = 44187.926| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 7.40 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9441 Z= 0.248 Angle : 0.708 11.771 12835 Z= 0.367 Chirality : 0.045 0.159 1426 Planarity : 0.005 0.041 1593 Dihedral : 7.617 59.460 1635 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.84 % Allowed : 20.08 % Favored : 74.08 % 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: -0.55 (0.24), residues: 1104 helix: 0.39 (0.24), residues: 432 sheet: -0.46 (0.34), residues: 212 loop : -0.93 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 36 HIS 0.021 0.002 HIS A 220 PHE 0.019 0.002 PHE R 230 TYR 0.020 0.002 TYR R 148 ARG 0.006 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 458) hydrogen bonds : angle 5.36203 ( 1302) SS BOND : bond 0.00476 ( 6) SS BOND : angle 1.04485 ( 12) covalent geometry : bond 0.00518 ( 9434) covalent geometry : angle 0.70723 (12823) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 0.947 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: A 41 HIS cc_start: 0.8034 (m90) cc_final: 0.7727 (m90) REVERT: A 219 PHE cc_start: 0.8920 (m-80) cc_final: 0.8403 (m-10) REVERT: B 59 TYR cc_start: 0.7707 (m-80) cc_final: 0.7054 (m-80) REVERT: B 105 TYR cc_start: 0.7851 (t80) cc_final: 0.7607 (t80) REVERT: B 188 MET cc_start: 0.8336 (mmp) cc_final: 0.7651 (mmp) REVERT: B 264 TYR cc_start: 0.8159 (m-80) cc_final: 0.7099 (m-80) REVERT: B 296 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8425 (m) REVERT: B 304 ARG cc_start: 0.8309 (mtp180) cc_final: 0.7892 (pmt-80) REVERT: B 325 MET cc_start: 0.8280 (mmm) cc_final: 0.7982 (mmm) REVERT: G 38 MET cc_start: 0.7904 (ptt) cc_final: 0.7571 (ptm) REVERT: N 76 LYS cc_start: 0.8284 (pttp) cc_final: 0.7843 (pttp) REVERT: N 80 TYR cc_start: 0.7948 (m-80) cc_final: 0.7466 (m-80) REVERT: R 269 TYR cc_start: 0.9040 (m-80) cc_final: 0.8215 (m-80) REVERT: R 357 ILE cc_start: 0.9616 (mm) cc_final: 0.9376 (mm) REVERT: R 393 PHE cc_start: 0.9062 (m-80) cc_final: 0.8595 (m-10) REVERT: R 397 MET cc_start: 0.9258 (mtm) cc_final: 0.8684 (ptm) outliers start: 57 outliers final: 41 residues processed: 166 average time/residue: 0.1952 time to fit residues: 45.9077 Evaluate side-chains 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain B residue 133 VAL 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 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 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 211 GLN 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 319 VAL 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: 0.6980 chunk 16 optimal weight: 0.0170 chunk 84 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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** N 31 ASN R 37 GLN R 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.094472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.073468 restraints weight = 43141.842| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 7.48 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9441 Z= 0.129 Angle : 0.645 12.858 12835 Z= 0.329 Chirality : 0.044 0.181 1426 Planarity : 0.004 0.035 1593 Dihedral : 7.125 59.887 1632 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.00 % Allowed : 22.85 % Favored : 73.16 % 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: -0.25 (0.25), residues: 1104 helix: 0.52 (0.24), residues: 436 sheet: -0.16 (0.35), residues: 192 loop : -0.71 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 36 HIS 0.007 0.001 HIS A 220 PHE 0.039 0.001 PHE N 29 TYR 0.015 0.002 TYR R 42 ARG 0.008 0.001 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 458) hydrogen bonds : angle 4.99394 ( 1302) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.76373 ( 12) covalent geometry : bond 0.00276 ( 9434) covalent geometry : angle 0.64499 (12823) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.8104 (m90) cc_final: 0.7887 (m-70) REVERT: A 219 PHE cc_start: 0.8972 (m-80) cc_final: 0.8403 (m-80) REVERT: A 279 ASN cc_start: 0.9647 (t0) cc_final: 0.9244 (t0) REVERT: B 59 TYR cc_start: 0.7329 (m-80) cc_final: 0.6789 (m-80) REVERT: B 75 GLN cc_start: 0.8531 (mm110) cc_final: 0.7962 (mm110) REVERT: B 188 MET cc_start: 0.8168 (mmp) cc_final: 0.7536 (mmp) REVERT: B 296 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8369 (m) REVERT: B 304 ARG cc_start: 0.8305 (mtp180) cc_final: 0.7816 (ppt170) REVERT: G 38 MET cc_start: 0.8010 (ptt) cc_final: 0.7616 (ptm) REVERT: N 80 TYR cc_start: 0.7976 (m-80) cc_final: 0.7624 (m-80) REVERT: R 269 TYR cc_start: 0.8978 (m-80) cc_final: 0.8228 (m-80) REVERT: R 357 ILE cc_start: 0.9583 (mm) cc_final: 0.9335 (mm) REVERT: R 393 PHE cc_start: 0.9036 (m-80) cc_final: 0.8463 (m-80) REVERT: R 394 GLN cc_start: 0.9092 (pt0) cc_final: 0.8664 (tt0) REVERT: R 397 MET cc_start: 0.9315 (mtm) cc_final: 0.8808 (ptp) REVERT: R 421 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8297 (mmm160) outliers start: 39 outliers final: 29 residues processed: 176 average time/residue: 0.2000 time to fit residues: 50.0634 Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 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 81 VAL 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 319 VAL 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: 1.9990 chunk 79 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.091853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.071031 restraints weight = 43566.139| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 7.41 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9441 Z= 0.177 Angle : 0.663 10.956 12835 Z= 0.336 Chirality : 0.044 0.161 1426 Planarity : 0.004 0.033 1593 Dihedral : 6.816 59.595 1631 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.23 % Allowed : 23.36 % Favored : 71.41 % 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: -0.13 (0.25), residues: 1104 helix: 0.68 (0.24), residues: 436 sheet: -0.24 (0.35), residues: 199 loop : -0.64 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP N 36 HIS 0.010 0.001 HIS A 220 PHE 0.025 0.002 PHE R 156 TYR 0.018 0.002 TYR R 42 ARG 0.006 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 458) hydrogen bonds : angle 4.99213 ( 1302) SS BOND : bond 0.00381 ( 6) SS BOND : angle 0.79799 ( 12) covalent geometry : bond 0.00382 ( 9434) covalent geometry : angle 0.66274 (12823) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 124 time to evaluate : 1.190 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: A 16 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8292 (mm-30) REVERT: A 41 HIS cc_start: 0.8014 (m90) cc_final: 0.7764 (m-70) REVERT: A 59 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.6058 (pp30) REVERT: A 219 PHE cc_start: 0.8969 (m-80) cc_final: 0.8377 (m-10) REVERT: A 221 MET cc_start: 0.9110 (tpp) cc_final: 0.8837 (tpp) REVERT: A 279 ASN cc_start: 0.9623 (t0) cc_final: 0.9252 (t0) REVERT: A 386 MET cc_start: 0.8794 (ppp) cc_final: 0.8437 (ppp) REVERT: A 388 LEU cc_start: 0.9108 (mm) cc_final: 0.8869 (mp) REVERT: B 59 TYR cc_start: 0.7613 (m-80) cc_final: 0.6874 (m-80) REVERT: B 188 MET cc_start: 0.8119 (mmp) cc_final: 0.7717 (mmp) REVERT: B 262 MET cc_start: 0.7287 (pmm) cc_final: 0.6899 (pmm) REVERT: B 296 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8469 (m) REVERT: B 304 ARG cc_start: 0.8285 (mtp180) cc_final: 0.7863 (ppt170) REVERT: G 38 MET cc_start: 0.8020 (ptt) cc_final: 0.7682 (ptm) REVERT: N 80 TYR cc_start: 0.8066 (m-80) cc_final: 0.7657 (m-80) REVERT: R 221 GLN cc_start: 0.9324 (mm110) cc_final: 0.8653 (pp30) REVERT: R 269 TYR cc_start: 0.9012 (m-80) cc_final: 0.8286 (m-80) REVERT: R 357 ILE cc_start: 0.9614 (mm) cc_final: 0.9376 (mm) REVERT: R 393 PHE cc_start: 0.9053 (m-80) cc_final: 0.8509 (m-80) REVERT: R 397 MET cc_start: 0.9327 (mtm) cc_final: 0.8789 (ptp) REVERT: R 421 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8278 (mmm160) outliers start: 51 outliers final: 35 residues processed: 162 average time/residue: 0.2724 time to fit residues: 62.8246 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 : 1.052 ------------------------------------------------------------------------------- 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 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 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 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 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 421 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.093261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.072223 restraints weight = 43610.686| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 7.44 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9441 Z= 0.136 Angle : 0.658 8.911 12835 Z= 0.330 Chirality : 0.044 0.215 1426 Planarity : 0.004 0.038 1593 Dihedral : 6.579 59.948 1631 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.41 % Allowed : 24.28 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.25), residues: 1104 helix: 0.95 (0.25), residues: 428 sheet: -0.22 (0.35), residues: 200 loop : -0.53 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 36 HIS 0.006 0.001 HIS A 220 PHE 0.023 0.001 PHE N 29 TYR 0.017 0.002 TYR R 42 ARG 0.005 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 458) hydrogen bonds : angle 4.89154 ( 1302) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.95339 ( 12) covalent geometry : bond 0.00300 ( 9434) covalent geometry : angle 0.65744 (12823) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 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: A 16 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8304 (mm-30) REVERT: A 41 HIS cc_start: 0.7945 (m90) cc_final: 0.7712 (m-70) REVERT: A 219 PHE cc_start: 0.8930 (m-80) cc_final: 0.8323 (m-10) REVERT: A 221 MET cc_start: 0.9108 (tpp) cc_final: 0.8871 (tpp) REVERT: A 279 ASN cc_start: 0.9607 (t0) cc_final: 0.9296 (t0) REVERT: A 386 MET cc_start: 0.8794 (ppp) cc_final: 0.8472 (ppp) REVERT: A 388 LEU cc_start: 0.9094 (mm) cc_final: 0.8815 (mp) REVERT: B 59 TYR cc_start: 0.7506 (m-80) cc_final: 0.7020 (m-80) REVERT: B 75 GLN cc_start: 0.8412 (mm110) cc_final: 0.7924 (mm110) REVERT: B 188 MET cc_start: 0.7938 (mmp) cc_final: 0.7736 (mmp) REVERT: B 246 ASP cc_start: 0.8828 (t0) cc_final: 0.8381 (t0) REVERT: B 262 MET cc_start: 0.7023 (pmm) cc_final: 0.6704 (pmm) REVERT: B 296 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8438 (m) REVERT: B 304 ARG cc_start: 0.8294 (mtp180) cc_final: 0.7847 (ppt170) REVERT: G 38 MET cc_start: 0.8025 (ptt) cc_final: 0.7737 (ptm) REVERT: N 80 TYR cc_start: 0.7977 (m-80) cc_final: 0.7542 (m-80) REVERT: R 221 GLN cc_start: 0.9326 (mm110) cc_final: 0.8675 (pp30) REVERT: R 243 TRP cc_start: 0.7979 (m100) cc_final: 0.7375 (m100) REVERT: R 269 TYR cc_start: 0.8977 (m-80) cc_final: 0.8232 (m-80) REVERT: R 357 ILE cc_start: 0.9600 (mm) cc_final: 0.9363 (mm) REVERT: R 393 PHE cc_start: 0.9003 (m-80) cc_final: 0.8334 (m-80) REVERT: R 397 MET cc_start: 0.9305 (mtm) cc_final: 0.8766 (mtm) outliers start: 43 outliers final: 36 residues processed: 159 average time/residue: 0.1926 time to fit residues: 44.8148 Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 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 N residue 125 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 142 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.091889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.071004 restraints weight = 44934.265| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 7.50 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9441 Z= 0.160 Angle : 0.652 8.158 12835 Z= 0.330 Chirality : 0.043 0.165 1426 Planarity : 0.004 0.033 1593 Dihedral : 6.191 59.863 1625 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.33 % Allowed : 24.08 % 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: 0.08 (0.25), residues: 1104 helix: 0.95 (0.24), residues: 436 sheet: -0.25 (0.34), residues: 210 loop : -0.57 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 277 HIS 0.009 0.001 HIS A 357 PHE 0.018 0.002 PHE R 230 TYR 0.018 0.002 TYR B 264 ARG 0.006 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 458) hydrogen bonds : angle 4.88462 ( 1302) SS BOND : bond 0.00214 ( 6) SS BOND : angle 1.27115 ( 12) covalent geometry : bond 0.00348 ( 9434) covalent geometry : angle 0.65143 (12823) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 1.052 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 216 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6452 (pttp) REVERT: A 219 PHE cc_start: 0.8944 (m-80) cc_final: 0.8403 (m-80) REVERT: A 279 ASN cc_start: 0.9625 (t0) cc_final: 0.9301 (t0) REVERT: A 386 MET cc_start: 0.8865 (ppp) cc_final: 0.8549 (ppp) REVERT: A 388 LEU cc_start: 0.9099 (mm) cc_final: 0.8757 (mp) REVERT: B 59 TYR cc_start: 0.7657 (m-80) cc_final: 0.6972 (m-80) REVERT: B 188 MET cc_start: 0.7977 (mmp) cc_final: 0.7723 (mmp) REVERT: B 198 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8112 (tp) REVERT: B 262 MET cc_start: 0.7093 (pmm) cc_final: 0.6797 (pmm) REVERT: B 296 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8489 (m) REVERT: B 304 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7933 (ppt170) REVERT: G 38 MET cc_start: 0.8035 (ptt) cc_final: 0.7761 (ptm) REVERT: N 80 TYR cc_start: 0.7917 (m-80) cc_final: 0.7468 (m-80) REVERT: R 179 ILE cc_start: 0.9553 (mm) cc_final: 0.9200 (mm) REVERT: R 243 TRP cc_start: 0.7938 (m100) cc_final: 0.7395 (m100) REVERT: R 269 TYR cc_start: 0.8989 (m-80) cc_final: 0.8206 (m-80) REVERT: R 357 ILE cc_start: 0.9616 (mm) cc_final: 0.9372 (mm) REVERT: R 393 PHE cc_start: 0.8999 (m-80) cc_final: 0.8289 (m-80) REVERT: R 397 MET cc_start: 0.9289 (mtm) cc_final: 0.8726 (mtm) outliers start: 52 outliers final: 39 residues processed: 158 average time/residue: 0.2047 time to fit residues: 46.9321 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 : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 235 ILE 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 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 N residue 111 THR Chi-restraints excluded: chain N residue 125 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 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: 1.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 49 optimal weight: 0.0470 chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 26 optimal weight: 0.0570 overall best weight: 1.6202 ------------------------------------------------------------------------------- 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 220 HIS ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.092311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.071910 restraints weight = 43488.013| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 7.34 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9441 Z= 0.148 Angle : 0.664 8.707 12835 Z= 0.332 Chirality : 0.043 0.149 1426 Planarity : 0.004 0.037 1593 Dihedral : 6.102 59.598 1625 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.82 % Allowed : 24.80 % 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: 0.09 (0.25), residues: 1104 helix: 1.03 (0.25), residues: 436 sheet: -0.26 (0.34), residues: 210 loop : -0.64 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 36 HIS 0.013 0.001 HIS B 142 PHE 0.018 0.001 PHE R 230 TYR 0.016 0.002 TYR B 289 ARG 0.005 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 458) hydrogen bonds : angle 4.84089 ( 1302) SS BOND : bond 0.00283 ( 6) SS BOND : angle 1.17807 ( 12) covalent geometry : bond 0.00323 ( 9434) covalent geometry : angle 0.66335 (12823) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 1.091 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 216 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6482 (pttp) REVERT: A 219 PHE cc_start: 0.8849 (m-80) cc_final: 0.8415 (m-80) REVERT: A 221 MET cc_start: 0.9176 (tpp) cc_final: 0.8888 (tpp) REVERT: A 279 ASN cc_start: 0.9615 (t0) cc_final: 0.9281 (t0) REVERT: A 386 MET cc_start: 0.8847 (ppp) cc_final: 0.8529 (ppp) REVERT: A 388 LEU cc_start: 0.9095 (mm) cc_final: 0.8760 (mp) REVERT: B 59 TYR cc_start: 0.7700 (m-80) cc_final: 0.7015 (m-80) REVERT: B 198 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8257 (mt) REVERT: B 262 MET cc_start: 0.7126 (pmm) cc_final: 0.6839 (pmm) REVERT: B 296 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8520 (m) REVERT: B 304 ARG cc_start: 0.8424 (mtp180) cc_final: 0.7998 (ppt170) REVERT: G 38 MET cc_start: 0.8024 (ptt) cc_final: 0.7784 (ptm) REVERT: N 80 TYR cc_start: 0.7935 (m-80) cc_final: 0.7484 (m-80) REVERT: N 95 TYR cc_start: 0.8793 (m-80) cc_final: 0.8564 (m-80) REVERT: R 143 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8193 (t80) REVERT: R 144 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9170 (pp) REVERT: R 243 TRP cc_start: 0.7988 (m100) cc_final: 0.7421 (m100) REVERT: R 269 TYR cc_start: 0.8989 (m-80) cc_final: 0.8192 (m-80) REVERT: R 357 ILE cc_start: 0.9616 (mm) cc_final: 0.9375 (mm) REVERT: R 393 PHE cc_start: 0.9007 (m-80) cc_final: 0.8286 (m-80) REVERT: R 397 MET cc_start: 0.9314 (mtm) cc_final: 0.8768 (mtm) outliers start: 47 outliers final: 39 residues processed: 158 average time/residue: 0.1927 time to fit residues: 43.7208 Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 235 ILE 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 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 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 N residue 111 THR Chi-restraints excluded: chain N residue 125 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 144 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 4 optimal weight: 0.0670 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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 B 142 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.093126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.072812 restraints weight = 43763.945| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 7.41 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9441 Z= 0.133 Angle : 0.682 9.516 12835 Z= 0.340 Chirality : 0.044 0.276 1426 Planarity : 0.004 0.038 1593 Dihedral : 6.036 58.343 1625 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.61 % Allowed : 25.00 % 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: 0.24 (0.26), residues: 1104 helix: 1.20 (0.25), residues: 429 sheet: -0.20 (0.35), residues: 208 loop : -0.58 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP A 277 HIS 0.008 0.001 HIS A 357 PHE 0.018 0.001 PHE R 230 TYR 0.021 0.002 TYR N 94 ARG 0.006 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 458) hydrogen bonds : angle 4.79117 ( 1302) SS BOND : bond 0.00244 ( 6) SS BOND : angle 1.13783 ( 12) covalent geometry : bond 0.00295 ( 9434) covalent geometry : angle 0.68178 (12823) Misc. bond : bond 0.00025 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 1.057 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 216 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6483 (pttp) REVERT: A 219 PHE cc_start: 0.8769 (m-80) cc_final: 0.8280 (m-10) REVERT: A 221 MET cc_start: 0.9201 (tpp) cc_final: 0.8909 (tpp) REVERT: A 279 ASN cc_start: 0.9593 (t0) cc_final: 0.9258 (t0) REVERT: A 386 MET cc_start: 0.8875 (ppp) cc_final: 0.8558 (ppp) REVERT: A 388 LEU cc_start: 0.9098 (mm) cc_final: 0.8762 (mp) REVERT: B 59 TYR cc_start: 0.7669 (m-80) cc_final: 0.7159 (m-80) REVERT: B 75 GLN cc_start: 0.8525 (mm110) cc_final: 0.8100 (mm110) REVERT: B 198 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8363 (mt) REVERT: B 262 MET cc_start: 0.7149 (pmm) cc_final: 0.6927 (pmm) REVERT: B 296 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8501 (m) REVERT: B 304 ARG cc_start: 0.8513 (mtp180) cc_final: 0.8032 (ppt170) REVERT: G 38 MET cc_start: 0.8052 (ptt) cc_final: 0.7817 (ptm) REVERT: N 80 TYR cc_start: 0.7863 (m-80) cc_final: 0.7422 (m-80) REVERT: N 95 TYR cc_start: 0.8778 (m-80) cc_final: 0.8532 (m-80) REVERT: R 143 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8203 (t80) REVERT: R 144 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9176 (pp) REVERT: R 243 TRP cc_start: 0.7915 (m100) cc_final: 0.7175 (m100) REVERT: R 269 TYR cc_start: 0.8974 (m-80) cc_final: 0.8191 (m-80) REVERT: R 357 ILE cc_start: 0.9593 (mm) cc_final: 0.9354 (mm) REVERT: R 393 PHE cc_start: 0.8957 (m-80) cc_final: 0.8239 (m-80) REVERT: R 397 MET cc_start: 0.9323 (mtm) cc_final: 0.8809 (mtm) REVERT: R 415 LYS cc_start: 0.9335 (tmtt) cc_final: 0.9077 (ptpt) outliers start: 45 outliers final: 37 residues processed: 160 average time/residue: 0.2050 time to fit residues: 46.6361 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 : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 235 ILE 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 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 337 LYS 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 N residue 125 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 144 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 4 optimal weight: 0.0040 chunk 84 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 B 142 HIS B 225 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.093951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.073662 restraints weight = 43351.444| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 7.33 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9441 Z= 0.127 Angle : 0.687 9.231 12835 Z= 0.339 Chirality : 0.044 0.241 1426 Planarity : 0.004 0.038 1593 Dihedral : 5.893 56.168 1625 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.10 % Allowed : 25.41 % 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: 0.27 (0.26), residues: 1104 helix: 1.25 (0.25), residues: 429 sheet: -0.10 (0.35), residues: 206 loop : -0.62 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP N 36 HIS 0.013 0.001 HIS B 225 PHE 0.018 0.001 PHE R 230 TYR 0.021 0.002 TYR N 94 ARG 0.004 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 458) hydrogen bonds : angle 4.71146 ( 1302) SS BOND : bond 0.00233 ( 6) SS BOND : angle 1.09437 ( 12) covalent geometry : bond 0.00279 ( 9434) covalent geometry : angle 0.68666 (12823) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5209.40 seconds wall clock time: 91 minutes 25.36 seconds (5485.36 seconds total)