Starting phenix.real_space_refine on Thu Feb 13 21:24:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dur_30867/02_2025/7dur_30867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dur_30867/02_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_30867/02_2025/7dur_30867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dur_30867/02_2025/7dur_30867.map" model { file = "/net/cci-nas-00/data/ceres_data/7dur_30867/02_2025/7dur_30867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dur_30867/02_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-5592/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: 5.51, per 1000 atoms: 0.60 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: 2.64 Conformation dependent library (CDL) restraints added in 1.0 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: 1.02 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: 2.44 Time building geometry restraints manager: 2.88 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: 0.710 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.880 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 9434 Z= 0.496 Angle : 1.094 11.361 12823 Z= 0.593 Chirality : 0.066 0.476 1426 Planarity : 0.007 0.055 1593 Dihedral : 15.688 89.376 3722 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.61 % Allowed : 7.79 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.23), residues: 1104 helix: -1.79 (0.21), residues: 433 sheet: -1.25 (0.32), residues: 201 loop : -1.46 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP R 87 HIS 0.011 0.002 HIS B 142 PHE 0.053 0.004 PHE R 280 TYR 0.034 0.004 TYR B 264 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 1.051 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: 0.2672 time to fit residues: 98.6802 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 : 1.033 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.074393 restraints weight = 43173.447| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 7.55 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9434 Z= 0.256 Angle : 0.740 7.830 12823 Z= 0.387 Chirality : 0.046 0.170 1426 Planarity : 0.005 0.043 1593 Dihedral : 9.449 77.575 1672 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.92 % Allowed : 15.68 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1104 helix: -0.28 (0.24), residues: 427 sheet: -0.85 (0.31), residues: 220 loop : -1.06 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 36 HIS 0.008 0.001 HIS B 225 PHE 0.031 0.002 PHE N 29 TYR 0.039 0.002 TYR N 32 ARG 0.007 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 1.028 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: 0.7454 (m-80) cc_final: 0.6985 (m-80) REVERT: B 61 MET cc_start: 0.7803 (ppp) cc_final: 0.7549 (ppp) REVERT: B 75 GLN cc_start: 0.9031 (mm110) cc_final: 0.8257 (mm110) REVERT: B 117 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8525 (mm) REVERT: B 188 MET cc_start: 0.8307 (mmp) cc_final: 0.7257 (mmp) REVERT: B 264 TYR cc_start: 0.8153 (m-80) cc_final: 0.7752 (m-80) REVERT: B 296 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8073 (m) REVERT: G 21 MET cc_start: 0.4792 (tmm) cc_final: 0.4498 (ttp) REVERT: G 38 MET cc_start: 0.7946 (ptt) cc_final: 0.7579 (ptm) REVERT: N 80 TYR cc_start: 0.8033 (m-80) cc_final: 0.7549 (m-80) REVERT: N 83 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.9111 (mmp) REVERT: R 221 GLN cc_start: 0.9337 (mm110) cc_final: 0.8683 (pp30) REVERT: R 269 TYR cc_start: 0.8951 (m-80) cc_final: 0.8004 (m-80) REVERT: R 353 THR cc_start: 0.9697 (m) cc_final: 0.9408 (p) REVERT: R 357 ILE cc_start: 0.9572 (mm) cc_final: 0.9321 (mm) REVERT: R 393 PHE cc_start: 0.9093 (m-80) cc_final: 0.8603 (m-10) REVERT: R 397 MET cc_start: 0.9248 (mtm) cc_final: 0.8770 (ptm) REVERT: R 418 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8778 (mm-30) REVERT: R 421 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8565 (mmm160) outliers start: 48 outliers final: 28 residues processed: 187 average time/residue: 0.2399 time to fit residues: 62.5832 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 : 1.084 ------------------------------------------------------------------------------- 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: 7.9990 chunk 88 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 6 optimal weight: 0.1980 chunk 69 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.092050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.071011 restraints weight = 43945.336| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 7.50 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9434 Z= 0.300 Angle : 0.711 10.823 12823 Z= 0.370 Chirality : 0.045 0.184 1426 Planarity : 0.005 0.044 1593 Dihedral : 8.215 72.126 1645 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.02 % Allowed : 18.44 % Favored : 76.54 % 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: -0.77 (0.24), residues: 1104 helix: 0.16 (0.24), residues: 434 sheet: -0.68 (0.34), residues: 212 loop : -0.93 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 36 HIS 0.006 0.002 HIS B 225 PHE 0.019 0.002 PHE R 280 TYR 0.021 0.002 TYR R 148 ARG 0.013 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 1.080 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 41 HIS cc_start: 0.8292 (m90) cc_final: 0.7984 (m90) REVERT: B 55 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 59 TYR cc_start: 0.7576 (m-80) cc_final: 0.6981 (m-80) REVERT: B 188 MET cc_start: 0.8445 (mmp) cc_final: 0.7545 (mmp) REVERT: B 296 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8443 (m) REVERT: B 304 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7844 (ppt170) REVERT: G 38 MET cc_start: 0.7897 (ptt) cc_final: 0.7586 (ptm) REVERT: N 80 TYR cc_start: 0.7870 (m-80) cc_final: 0.7077 (m-80) REVERT: R 269 TYR cc_start: 0.8981 (m-80) cc_final: 0.8151 (m-80) REVERT: R 357 ILE cc_start: 0.9608 (mm) cc_final: 0.9364 (mm) REVERT: R 393 PHE cc_start: 0.9072 (m-80) cc_final: 0.8572 (m-10) REVERT: R 397 MET cc_start: 0.9243 (mtm) cc_final: 0.8767 (ptm) outliers start: 49 outliers final: 35 residues processed: 162 average time/residue: 0.2140 time to fit residues: 48.3845 Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 111 THR 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 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 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: 7.9990 chunk 81 optimal weight: 7.9990 chunk 65 optimal weight: 0.0170 chunk 54 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 93 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.095193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.074125 restraints weight = 43331.102| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 7.58 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9434 Z= 0.178 Angle : 0.663 13.040 12823 Z= 0.335 Chirality : 0.043 0.180 1426 Planarity : 0.004 0.035 1593 Dihedral : 7.512 59.795 1637 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.20 % Allowed : 21.62 % Favored : 74.18 % 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: -0.41 (0.24), residues: 1104 helix: 0.47 (0.24), residues: 431 sheet: -0.36 (0.35), residues: 195 loop : -0.82 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 36 HIS 0.011 0.001 HIS A 220 PHE 0.020 0.002 PHE R 230 TYR 0.020 0.002 TYR R 88 ARG 0.005 0.000 ARG R 419 *********************** 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 186 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 1.096 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: 0.8168 (m90) cc_final: 0.7941 (m-70) REVERT: A 219 PHE cc_start: 0.8912 (m-80) cc_final: 0.8375 (m-10) REVERT: B 59 TYR cc_start: 0.7279 (m-80) cc_final: 0.6738 (m-80) REVERT: B 75 GLN cc_start: 0.8809 (mm110) cc_final: 0.8074 (mm110) REVERT: B 221 THR cc_start: 0.9318 (m) cc_final: 0.9080 (p) REVERT: B 226 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6442 (mp0) REVERT: B 296 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8325 (m) REVERT: B 304 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7643 (ppt170) REVERT: B 325 MET cc_start: 0.8033 (mmm) cc_final: 0.7761 (mmm) REVERT: G 38 MET cc_start: 0.7970 (ptt) cc_final: 0.7591 (ptm) REVERT: N 38 ARG cc_start: 0.8742 (ptm-80) cc_final: 0.8525 (ptm-80) REVERT: N 80 TYR cc_start: 0.7978 (m-80) cc_final: 0.7567 (m-80) REVERT: N 93 VAL cc_start: 0.9117 (p) cc_final: 0.8803 (t) REVERT: N 123 GLN cc_start: 0.8303 (tp-100) cc_final: 0.7893 (tp40) REVERT: R 269 TYR cc_start: 0.8968 (m-80) cc_final: 0.8212 (m-80) REVERT: R 357 ILE cc_start: 0.9589 (mm) cc_final: 0.9346 (mm) REVERT: R 393 PHE cc_start: 0.9007 (m-80) cc_final: 0.8480 (m-80) REVERT: R 394 GLN cc_start: 0.9070 (pt0) cc_final: 0.8673 (tt0) REVERT: R 397 MET cc_start: 0.9229 (mtm) cc_final: 0.8745 (ptm) REVERT: R 421 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8327 (mmm160) outliers start: 41 outliers final: 28 residues processed: 175 average time/residue: 0.2049 time to fit residues: 50.5350 Evaluate side-chains 147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN 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 = 0.4330 r_free = 0.4330 target = 0.094841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.074235 restraints weight = 43124.281| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 7.40 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9434 Z= 0.184 Angle : 0.643 12.337 12823 Z= 0.327 Chirality : 0.043 0.157 1426 Planarity : 0.004 0.034 1593 Dihedral : 7.029 59.825 1631 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.10 % Allowed : 22.95 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1104 helix: 0.70 (0.24), residues: 429 sheet: -0.33 (0.34), residues: 202 loop : -0.72 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 36 HIS 0.012 0.001 HIS A 220 PHE 0.019 0.001 PHE R 280 TYR 0.020 0.002 TYR R 42 ARG 0.005 0.000 ARG A 228 *********************** 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 178 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 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 41 HIS cc_start: 0.8167 (m90) cc_final: 0.7904 (m-70) REVERT: A 219 PHE cc_start: 0.8957 (m-80) cc_final: 0.8450 (m-10) REVERT: B 59 TYR cc_start: 0.7254 (m-80) cc_final: 0.6650 (m-80) REVERT: B 75 GLN cc_start: 0.8693 (mm110) cc_final: 0.7934 (mm110) REVERT: B 221 THR cc_start: 0.9342 (m) cc_final: 0.9104 (p) REVERT: B 226 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6408 (mp0) REVERT: B 262 MET cc_start: 0.5935 (ptm) cc_final: 0.5409 (pmm) REVERT: B 296 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8330 (m) REVERT: B 304 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7599 (ppt170) REVERT: B 325 MET cc_start: 0.8178 (mmm) cc_final: 0.7950 (mmm) REVERT: G 38 MET cc_start: 0.8088 (ptt) cc_final: 0.7784 (ptm) REVERT: N 80 TYR cc_start: 0.7913 (m-80) cc_final: 0.7571 (m-80) REVERT: R 179 ILE cc_start: 0.9546 (mm) cc_final: 0.9184 (mm) REVERT: R 221 GLN cc_start: 0.9300 (mm110) cc_final: 0.8429 (tm-30) REVERT: R 243 TRP cc_start: 0.7872 (m100) cc_final: 0.7494 (m100) REVERT: R 269 TYR cc_start: 0.8952 (m-80) cc_final: 0.8192 (m-80) REVERT: R 357 ILE cc_start: 0.9606 (mm) cc_final: 0.9373 (mm) REVERT: R 393 PHE cc_start: 0.9001 (m-80) cc_final: 0.8503 (m-80) REVERT: R 394 GLN cc_start: 0.9073 (pt0) cc_final: 0.8619 (tt0) REVERT: R 397 MET cc_start: 0.9266 (mtm) cc_final: 0.8782 (ptm) outliers start: 40 outliers final: 33 residues processed: 165 average time/residue: 0.1967 time to fit residues: 46.6063 Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 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 46 GLU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 264 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 = 0.4343 r_free = 0.4343 target = 0.095194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.074279 restraints weight = 43705.651| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 7.57 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9434 Z= 0.176 Angle : 0.650 12.277 12823 Z= 0.323 Chirality : 0.043 0.207 1426 Planarity : 0.004 0.035 1593 Dihedral : 6.699 59.850 1627 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.61 % Allowed : 23.77 % Favored : 71.62 % 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: 0.01 (0.25), residues: 1104 helix: 0.93 (0.25), residues: 429 sheet: -0.25 (0.34), residues: 208 loop : -0.65 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP N 36 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 280 TYR 0.016 0.002 TYR B 289 ARG 0.003 0.000 ARG B 150 *********************** 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 181 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.8088 (m90) cc_final: 0.7865 (m-70) REVERT: A 219 PHE cc_start: 0.8967 (m-80) cc_final: 0.8410 (m-80) REVERT: A 221 MET cc_start: 0.9067 (tpp) cc_final: 0.8750 (tpp) REVERT: B 59 TYR cc_start: 0.7249 (m-80) cc_final: 0.6593 (m-80) REVERT: B 75 GLN cc_start: 0.8679 (mm110) cc_final: 0.8065 (mm110) REVERT: B 262 MET cc_start: 0.5899 (ptm) cc_final: 0.5453 (pmm) REVERT: B 296 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8166 (m) REVERT: B 304 ARG cc_start: 0.8335 (mtp180) cc_final: 0.7714 (ppt170) REVERT: G 38 MET cc_start: 0.8141 (ptt) cc_final: 0.7832 (ptm) REVERT: N 80 TYR cc_start: 0.8029 (m-80) cc_final: 0.7581 (m-80) REVERT: R 179 ILE cc_start: 0.9541 (mm) cc_final: 0.9200 (mm) REVERT: R 221 GLN cc_start: 0.9286 (mm110) cc_final: 0.8392 (tm-30) REVERT: R 243 TRP cc_start: 0.7860 (m100) cc_final: 0.7391 (m100) REVERT: R 269 TYR cc_start: 0.8931 (m-80) cc_final: 0.8195 (m-80) REVERT: R 357 ILE cc_start: 0.9585 (mm) cc_final: 0.9347 (mm) REVERT: R 393 PHE cc_start: 0.8930 (m-80) cc_final: 0.8372 (m-80) REVERT: R 394 GLN cc_start: 0.9072 (pt0) cc_final: 0.8574 (tt0) REVERT: R 397 MET cc_start: 0.9260 (mtm) cc_final: 0.8791 (ptp) REVERT: R 415 LYS cc_start: 0.9290 (tmtt) cc_final: 0.9028 (ptpp) outliers start: 45 outliers final: 33 residues processed: 170 average time/residue: 0.2190 time to fit residues: 52.8073 Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 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 N residue 61 THR Chi-restraints excluded: chain N residue 125 THR 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 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 180 HIS Chi-restraints excluded: chain R residue 188 ILE 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 319 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 213 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.092994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.072242 restraints weight = 43618.176| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 7.51 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9434 Z= 0.229 Angle : 0.673 13.866 12823 Z= 0.338 Chirality : 0.043 0.148 1426 Planarity : 0.004 0.032 1593 Dihedral : 6.496 59.995 1627 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: 0.02 (0.25), residues: 1104 helix: 1.01 (0.25), residues: 435 sheet: -0.21 (0.35), residues: 198 loop : -0.76 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 36 HIS 0.022 0.002 HIS A 220 PHE 0.023 0.002 PHE B 235 TYR 0.016 0.002 TYR R 148 ARG 0.003 0.000 ARG B 150 *********************** 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 180 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 1.008 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: 0.8111 (m90) cc_final: 0.7906 (m-70) REVERT: A 59 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6114 (pp30) REVERT: A 219 PHE cc_start: 0.8944 (m-80) cc_final: 0.8267 (m-80) REVERT: B 59 TYR cc_start: 0.7308 (m-80) cc_final: 0.6739 (m-80) REVERT: B 75 GLN cc_start: 0.8711 (mm110) cc_final: 0.8140 (mm110) REVERT: B 262 MET cc_start: 0.5916 (ptm) cc_final: 0.5566 (pmm) REVERT: B 296 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8363 (m) REVERT: B 304 ARG cc_start: 0.8408 (mtp180) cc_final: 0.7855 (ppt170) REVERT: G 38 MET cc_start: 0.8178 (ptt) cc_final: 0.7906 (ptm) REVERT: N 80 TYR cc_start: 0.7980 (m-80) cc_final: 0.7595 (m-80) REVERT: N 81 LEU cc_start: 0.8934 (pp) cc_final: 0.8719 (pt) REVERT: R 179 ILE cc_start: 0.9556 (mm) cc_final: 0.9223 (mm) REVERT: R 221 GLN cc_start: 0.9321 (mm110) cc_final: 0.8443 (tm-30) REVERT: R 243 TRP cc_start: 0.7988 (m100) cc_final: 0.7430 (m100) REVERT: R 269 TYR cc_start: 0.8979 (m-80) cc_final: 0.8130 (m-80) REVERT: R 357 ILE cc_start: 0.9605 (mm) cc_final: 0.9368 (mm) REVERT: R 393 PHE cc_start: 0.8978 (m-80) cc_final: 0.8388 (m-80) REVERT: R 397 MET cc_start: 0.9239 (mtm) cc_final: 0.8816 (ptp) REVERT: R 421 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8278 (mmm160) outliers start: 51 outliers final: 41 residues processed: 168 average time/residue: 0.2025 time to fit residues: 48.3959 Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 277 TRP 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 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 G residue 28 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 125 THR 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 152 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 180 HIS Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 194 VAL 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 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.093455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.072785 restraints weight = 44090.158| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 7.43 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9434 Z= 0.207 Angle : 0.687 14.239 12823 Z= 0.341 Chirality : 0.043 0.230 1426 Planarity : 0.004 0.032 1593 Dihedral : 6.355 59.892 1627 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.92 % Allowed : 23.87 % Favored : 71.21 % 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: 0.15 (0.25), residues: 1104 helix: 1.20 (0.25), residues: 428 sheet: -0.31 (0.35), residues: 208 loop : -0.66 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N 36 HIS 0.004 0.001 HIS B 311 PHE 0.016 0.001 PHE R 280 TYR 0.019 0.002 TYR N 94 ARG 0.004 0.000 ARG N 98 *********************** 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: 48 poor density : 123 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.8113 (m90) cc_final: 0.7898 (m-70) REVERT: A 59 GLN cc_start: 0.6706 (OUTLIER) cc_final: 0.6227 (pp30) REVERT: A 219 PHE cc_start: 0.8954 (m-80) cc_final: 0.8368 (m-80) REVERT: A 220 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8263 (t-170) REVERT: A 388 LEU cc_start: 0.9081 (mm) cc_final: 0.8788 (mp) REVERT: B 59 TYR cc_start: 0.7280 (m-80) cc_final: 0.6777 (m-80) REVERT: B 75 GLN cc_start: 0.8704 (mm110) cc_final: 0.8166 (mm110) REVERT: B 226 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6137 (mp0) REVERT: B 262 MET cc_start: 0.5591 (ptm) cc_final: 0.5341 (pmm) REVERT: B 296 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8369 (m) REVERT: B 304 ARG cc_start: 0.8309 (mtp180) cc_final: 0.7818 (ppt170) REVERT: G 38 MET cc_start: 0.8127 (ptt) cc_final: 0.7880 (ptm) REVERT: N 80 TYR cc_start: 0.7891 (m-80) cc_final: 0.7547 (m-80) REVERT: R 144 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9313 (pp) REVERT: R 179 ILE cc_start: 0.9552 (mm) cc_final: 0.9196 (mm) REVERT: R 221 GLN cc_start: 0.9320 (mm110) cc_final: 0.8462 (tm-30) REVERT: R 243 TRP cc_start: 0.7961 (m100) cc_final: 0.7418 (m100) REVERT: R 269 TYR cc_start: 0.8975 (m-80) cc_final: 0.8193 (m-80) REVERT: R 357 ILE cc_start: 0.9596 (mm) cc_final: 0.9354 (mm) REVERT: R 393 PHE cc_start: 0.8915 (m-80) cc_final: 0.8366 (m-80) REVERT: R 397 MET cc_start: 0.9216 (mtm) cc_final: 0.8760 (ptp) outliers start: 48 outliers final: 36 residues processed: 163 average time/residue: 0.1957 time to fit residues: 45.6828 Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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 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 G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 110 VAL 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 144 LEU Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 180 HIS Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 194 VAL 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 319 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 97 optimal weight: 0.4980 chunk 26 optimal weight: 7.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.090941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.070355 restraints weight = 44270.915| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 7.22 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9434 Z= 0.274 Angle : 0.700 11.775 12823 Z= 0.355 Chirality : 0.045 0.279 1426 Planarity : 0.004 0.031 1593 Dihedral : 6.398 59.398 1627 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.51 % Allowed : 24.59 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.02 (0.25), residues: 1104 helix: 1.09 (0.25), residues: 436 sheet: -0.38 (0.35), residues: 218 loop : -0.76 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 277 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.002 PHE R 280 TYR 0.016 0.002 TYR R 148 ARG 0.011 0.001 ARG R 380 *********************** 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 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.991 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 219 PHE cc_start: 0.8938 (m-80) cc_final: 0.8330 (m-80) REVERT: A 220 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8202 (t-170) REVERT: B 59 TYR cc_start: 0.7553 (m-80) cc_final: 0.6820 (m-80) REVERT: B 226 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6169 (mp0) REVERT: B 296 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8504 (m) REVERT: B 304 ARG cc_start: 0.8485 (mtp180) cc_final: 0.7987 (pmt-80) REVERT: G 38 MET cc_start: 0.8188 (ptt) cc_final: 0.7919 (ptm) REVERT: N 80 TYR cc_start: 0.7877 (m-80) cc_final: 0.7416 (m-80) REVERT: R 221 GLN cc_start: 0.9348 (mm110) cc_final: 0.8423 (tm-30) REVERT: R 269 TYR cc_start: 0.9065 (m-80) cc_final: 0.8277 (m-80) REVERT: R 334 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8369 (tptt) REVERT: R 357 ILE cc_start: 0.9595 (mm) cc_final: 0.9357 (mm) REVERT: R 393 PHE cc_start: 0.8952 (m-80) cc_final: 0.8393 (m-80) REVERT: R 397 MET cc_start: 0.9196 (mtm) cc_final: 0.8740 (ptp) REVERT: R 415 LYS cc_start: 0.9336 (tmtt) cc_final: 0.9086 (ptpt) REVERT: R 421 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8306 (mmm160) outliers start: 44 outliers final: 34 residues processed: 151 average time/residue: 0.2013 time to fit residues: 43.3682 Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 110 VAL 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 154 LEU Chi-restraints excluded: chain R residue 188 ILE 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 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.093279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.072813 restraints weight = 43264.086| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 7.29 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9434 Z= 0.185 Angle : 0.715 11.329 12823 Z= 0.353 Chirality : 0.044 0.239 1426 Planarity : 0.004 0.033 1593 Dihedral : 6.210 57.658 1627 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.69 % Allowed : 25.61 % Favored : 70.70 % 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: 0.19 (0.26), residues: 1104 helix: 1.27 (0.25), residues: 428 sheet: -0.19 (0.35), residues: 216 loop : -0.76 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 36 HIS 0.004 0.001 HIS B 311 PHE 0.017 0.001 PHE N 27 TYR 0.021 0.002 TYR N 94 ARG 0.013 0.001 ARG N 98 ********************** 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 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.105 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 219 PHE cc_start: 0.8882 (m-80) cc_final: 0.8245 (m-80) REVERT: A 220 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.8178 (t-170) REVERT: A 388 LEU cc_start: 0.9141 (mm) cc_final: 0.8876 (mp) REVERT: B 59 TYR cc_start: 0.7441 (m-80) cc_final: 0.6940 (m-80) REVERT: B 75 GLN cc_start: 0.8712 (mm110) cc_final: 0.8251 (mm110) REVERT: B 226 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6291 (mp0) REVERT: B 262 MET cc_start: 0.6923 (pmm) cc_final: 0.5945 (ptt) REVERT: B 304 ARG cc_start: 0.8413 (mtp180) cc_final: 0.7831 (pmt-80) REVERT: G 38 MET cc_start: 0.8132 (ptt) cc_final: 0.7900 (ptm) REVERT: N 80 TYR cc_start: 0.7792 (m-80) cc_final: 0.7314 (m-80) REVERT: N 109 ASP cc_start: 0.4624 (m-30) cc_final: 0.4206 (m-30) REVERT: R 269 TYR cc_start: 0.9008 (m-80) cc_final: 0.8248 (m-80) REVERT: R 357 ILE cc_start: 0.9572 (mm) cc_final: 0.9337 (mm) REVERT: R 393 PHE cc_start: 0.8874 (m-80) cc_final: 0.8278 (m-80) REVERT: R 397 MET cc_start: 0.9256 (mtm) cc_final: 0.8767 (ptp) REVERT: R 415 LYS cc_start: 0.9345 (tmtt) cc_final: 0.9096 (ptpt) outliers start: 36 outliers final: 31 residues processed: 150 average time/residue: 0.1995 time to fit residues: 43.6621 Evaluate side-chains 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 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 G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 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 319 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 239 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.091675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.071882 restraints weight = 43827.258| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 7.26 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9434 Z= 0.223 Angle : 0.707 10.994 12823 Z= 0.351 Chirality : 0.044 0.240 1426 Planarity : 0.004 0.035 1593 Dihedral : 6.111 59.513 1627 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.89 % Allowed : 26.02 % Favored : 70.08 % 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: 0.13 (0.26), residues: 1104 helix: 1.24 (0.25), residues: 437 sheet: -0.18 (0.35), residues: 216 loop : -0.86 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP N 36 HIS 0.004 0.001 HIS A 362 PHE 0.020 0.002 PHE B 278 TYR 0.022 0.002 TYR N 32 ARG 0.003 0.000 ARG N 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4795.16 seconds wall clock time: 85 minutes 59.27 seconds (5159.27 seconds total)