Starting phenix.real_space_refine on Fri Jul 3 15:10:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ps5_17845/07_2026/8ps5_17845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps5_17845/07_2026/8ps5_17845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ps5_17845/07_2026/8ps5_17845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps5_17845/07_2026/8ps5_17845.map" model { file = "/net/cci-nas-00/data/ceres_data/8ps5_17845/07_2026/8ps5_17845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps5_17845/07_2026/8ps5_17845.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 P 78 5.49 5 S 40 5.16 5 C 9276 2.51 5 N 2550 2.21 5 O 2942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14886 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3324 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 15, 'TRANS': 392} Chain: "B" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3324 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 15, 'TRANS': 392} Chain: "C" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3302 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Chain: "D" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3302 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 817 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 817 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Time building chain proxies: 3.57, per 1000 atoms: 0.24 Number of scatterers: 14886 At special positions: 0 Unit cell: (97.5, 89.7, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 78 15.00 O 2942 8.00 N 2550 7.00 C 9276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 711.4 milliseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 45.6% alpha, 14.9% beta 38 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 23 through 33 removed outlier: 4.353A pdb=" N TRP A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 removed outlier: 3.817A pdb=" N PHE A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.512A pdb=" N ARG A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.724A pdb=" N LYS A 193 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 221 Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 305 through 326 removed outlier: 3.683A pdb=" N GLY A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 391 through 408 removed outlier: 3.622A pdb=" N GLY A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 34 removed outlier: 4.028A pdb=" N TRP B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 4.332A pdb=" N PHE B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.817A pdb=" N ARG B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 148 through 168 Processing helix chain 'B' and resid 172 through 189 Processing helix chain 'B' and resid 195 through 221 Processing helix chain 'B' and resid 225 through 234 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 305 through 326 removed outlier: 3.617A pdb=" N GLY B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'B' and resid 369 through 381 Processing helix chain 'B' and resid 391 through 408 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.033A pdb=" N VAL C 108 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 148 through 164 removed outlier: 3.527A pdb=" N VAL C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 183 removed outlier: 3.791A pdb=" N ARG C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 removed outlier: 3.737A pdb=" N LEU C 202 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 224 removed outlier: 3.586A pdb=" N LEU C 224 " --> pdb=" O LYS C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 225 through 241 removed outlier: 3.505A pdb=" N LEU C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 4.660A pdb=" N THR C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 324 Processing helix chain 'C' and resid 326 through 337 removed outlier: 3.503A pdb=" N GLU C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 381 removed outlier: 3.620A pdb=" N GLU C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 378 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS C 380 " --> pdb=" O PHE C 376 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 381 " --> pdb=" O GLU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 408 removed outlier: 3.635A pdb=" N GLY C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 34 Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.920A pdb=" N PHE D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 118 removed outlier: 4.223A pdb=" N ARG D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 148 through 168 Processing helix chain 'D' and resid 171 through 189 removed outlier: 3.503A pdb=" N ARG D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 221 Processing helix chain 'D' and resid 225 through 234 Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 305 through 337 removed outlier: 3.552A pdb=" N GLY D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 381 removed outlier: 3.607A pdb=" N ARG D 381 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 6.603A pdb=" N VAL A 11 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 64 " --> pdb=" O TYR A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 255 removed outlier: 4.850A pdb=" N ILE A 245 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP A 274 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 247 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 272 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU A 249 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE A 270 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 12.285A pdb=" N ILE A 268 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N VAL A 284 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 270 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA A 354 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU A 390 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE A 356 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.601A pdb=" N GLN B 3 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET B 13 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASN B 67 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N TYR B 15 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER B 65 " --> pdb=" O TYR B 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AA6, first strand: chain 'B' and resid 244 through 255 removed outlier: 6.414A pdb=" N VAL B 273 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 247 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 271 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU B 249 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASP B 269 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL B 251 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE B 267 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 253 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN B 265 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 12.087A pdb=" N ILE B 268 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N VAL B 284 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 270 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 354 " --> pdb=" O ASP B 388 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU B 390 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE B 356 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 36 through 38 Processing sheet with id=AA9, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.720A pdb=" N THR C 70 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 244 through 255 removed outlier: 4.923A pdb=" N ILE C 245 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP C 274 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C 247 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU C 272 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 249 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 270 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 12.151A pdb=" N ILE C 268 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N VAL C 284 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE C 270 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 354 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU C 390 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 356 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 15 removed outlier: 6.381A pdb=" N VAL D 11 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 35 through 38 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.355A pdb=" N LEU D 90 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 244 through 255 removed outlier: 6.648A pdb=" N VAL D 273 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 247 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA D 271 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU D 249 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP D 269 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL D 251 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE D 267 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 253 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN D 265 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 12.348A pdb=" N ILE D 268 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N VAL D 284 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE D 270 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA D 354 " --> pdb=" O ASP D 388 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU D 390 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE D 356 " --> pdb=" O LEU D 390 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3528 1.33 - 1.45: 3341 1.45 - 1.57: 8240 1.57 - 1.69: 157 1.69 - 1.81: 72 Bond restraints: 15338 Sorted by residual: bond pdb=" C3' DG E 31 " pdb=" C2' DG E 31 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" N GLY D 69 " pdb=" CA GLY D 69 " ideal model delta sigma weight residual 1.446 1.477 -0.031 9.70e-03 1.06e+04 1.00e+01 bond pdb=" C3' DA E 23 " pdb=" O3' DA E 23 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.83e+00 bond pdb=" N ASP B 169 " pdb=" CA ASP B 169 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.58e+00 bond pdb=" N LYS A 221 " pdb=" CA LYS A 221 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.55e+00 ... (remaining 15333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 20346 2.35 - 4.69: 629 4.69 - 7.04: 73 7.04 - 9.39: 14 9.39 - 11.73: 6 Bond angle restraints: 21068 Sorted by residual: angle pdb=" CA GLY D 69 " pdb=" C GLY D 69 " pdb=" O GLY D 69 " ideal model delta sigma weight residual 122.22 117.96 4.26 6.50e-01 2.37e+00 4.30e+01 angle pdb=" C ARG A 294 " pdb=" N LYS A 295 " pdb=" CA LYS A 295 " ideal model delta sigma weight residual 121.54 133.27 -11.73 1.91e+00 2.74e-01 3.77e+01 angle pdb=" C ASP B 169 " pdb=" CA ASP B 169 " pdb=" CB ASP B 169 " ideal model delta sigma weight residual 110.06 118.42 -8.36 1.44e+00 4.82e-01 3.37e+01 angle pdb=" C SER C 39 " pdb=" N ARG C 40 " pdb=" CA ARG C 40 " ideal model delta sigma weight residual 121.54 132.55 -11.01 1.91e+00 2.74e-01 3.32e+01 angle pdb=" C ARG C 189 " pdb=" N LYS C 190 " pdb=" CA LYS C 190 " ideal model delta sigma weight residual 121.54 132.36 -10.82 1.91e+00 2.74e-01 3.21e+01 ... (remaining 21063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 8420 34.68 - 69.36: 678 69.36 - 104.03: 28 104.03 - 138.71: 0 138.71 - 173.39: 2 Dihedral angle restraints: 9128 sinusoidal: 4342 harmonic: 4786 Sorted by residual: dihedral pdb=" C ASP B 169 " pdb=" N ASP B 169 " pdb=" CA ASP B 169 " pdb=" CB ASP B 169 " ideal model delta harmonic sigma weight residual -122.60 -137.36 14.76 0 2.50e+00 1.60e-01 3.49e+01 dihedral pdb=" N ASP B 169 " pdb=" C ASP B 169 " pdb=" CA ASP B 169 " pdb=" CB ASP B 169 " ideal model delta harmonic sigma weight residual 122.80 135.31 -12.51 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" CA GLY D 359 " pdb=" C GLY D 359 " pdb=" N ARG D 360 " pdb=" CA ARG D 360 " ideal model delta harmonic sigma weight residual -180.00 -156.20 -23.80 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 9125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2261 0.132 - 0.263: 93 0.263 - 0.395: 2 0.395 - 0.526: 1 0.526 - 0.658: 1 Chirality restraints: 2358 Sorted by residual: chirality pdb=" CB ILE B 245 " pdb=" CA ILE B 245 " pdb=" CG1 ILE B 245 " pdb=" CG2 ILE B 245 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA ASP B 169 " pdb=" N ASP B 169 " pdb=" C ASP B 169 " pdb=" CB ASP B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CA ILE D 234 " pdb=" N ILE D 234 " pdb=" C ILE D 234 " pdb=" CB ILE D 234 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2355 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 40 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C ARG C 40 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG C 40 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C 41 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 121 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C THR B 121 " -0.048 2.00e-02 2.50e+03 pdb=" O THR B 121 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 122 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 121 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C THR A 121 " 0.043 2.00e-02 2.50e+03 pdb=" O THR A 121 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 122 " -0.014 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1723 2.76 - 3.29: 13082 3.29 - 3.83: 25806 3.83 - 4.36: 31051 4.36 - 4.90: 51078 Nonbonded interactions: 122740 Sorted by model distance: nonbonded pdb=" OD2 ASP D 255 " pdb=" OG1 THR D 264 " model vdw 2.221 3.040 nonbonded pdb=" O ARG D 113 " pdb=" CD1 LEU D 117 " model vdw 2.226 3.460 nonbonded pdb=" NZ LYS B 263 " pdb=" OP2 DG F 22 " model vdw 2.286 3.120 nonbonded pdb=" O SER D 350 " pdb=" OG SER D 350 " model vdw 2.316 3.040 nonbonded pdb=" OE1 GLU A 330 " pdb=" OH TYR C 257 " model vdw 2.338 3.040 ... (remaining 122735 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 16 or resid 21 through 408)) selection = (chain 'B' and (resid 1 through 16 or resid 21 through 408)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.880 Find NCS groups from input model: 0.300 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:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.006 0.076 15338 Z= 0.412 Angle : 0.965 11.734 21068 Z= 0.636 Chirality : 0.060 0.658 2358 Planarity : 0.007 0.058 2420 Dihedral : 21.091 173.390 6032 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.49 % Allowed : 23.17 % Favored : 75.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.17), residues: 1612 helix: -2.66 (0.13), residues: 701 sheet: -0.22 (0.35), residues: 240 loop : -1.15 (0.20), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 299 TYR 0.016 0.002 TYR B 244 PHE 0.032 0.002 PHE A 44 TRP 0.028 0.003 TRP A 325 HIS 0.007 0.002 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.41 (15338) covalent geometry : angle 0.96478 / 0.64 (21068) hydrogen bonds : bond 0.19076 / 12.32 ( 697) hydrogen bonds : angle 7.73830 / 5.56 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.418 Fit side-chains REVERT: A 3 GLN cc_start: 0.7912 (mt0) cc_final: 0.7467 (mt0) REVERT: A 338 LYS cc_start: 0.7996 (pttp) cc_final: 0.7469 (mttm) REVERT: A 346 CYS cc_start: 0.8350 (m) cc_final: 0.8005 (p) REVERT: B 23 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8144 (tp) REVERT: B 386 MET cc_start: 0.8970 (mmt) cc_final: 0.7594 (mmt) REVERT: C 13 MET cc_start: 0.7655 (mmt) cc_final: 0.7455 (mmt) REVERT: C 394 ASP cc_start: 0.7934 (t0) cc_final: 0.7639 (t0) REVERT: D 13 MET cc_start: 0.4157 (ptm) cc_final: 0.3871 (ppp) REVERT: D 362 GLN cc_start: 0.8289 (pt0) cc_final: 0.7840 (pm20) outliers start: 22 outliers final: 13 residues processed: 175 average time/residue: 0.6025 time to fit residues: 116.0491 Evaluate side-chains 132 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 369 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 143 GLN B 45 GLN B 362 GLN C 43 ASN C 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.174058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106620 restraints weight = 17038.885| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.18 r_work: 0.3157 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15338 Z= 0.122 Angle : 0.535 7.522 21068 Z= 0.305 Chirality : 0.043 0.224 2358 Planarity : 0.004 0.037 2420 Dihedral : 20.775 177.071 2678 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.66 % Allowed : 23.10 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 1612 helix: 0.14 (0.17), residues: 696 sheet: -0.23 (0.35), residues: 228 loop : -0.73 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 299 TYR 0.015 0.001 TYR B 392 PHE 0.017 0.001 PHE C 4 TRP 0.007 0.001 TRP C 25 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (15338) covalent geometry : angle 0.53513 / 0.30 (21068) hydrogen bonds : bond 0.04333 / 2.79 ( 697) hydrogen bonds : angle 4.72912 / 3.38 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 0.585 Fit side-chains REVERT: A 1 MET cc_start: 0.3415 (tpp) cc_final: 0.3202 (tpt) REVERT: A 3 GLN cc_start: 0.7467 (mt0) cc_final: 0.7072 (mt0) REVERT: A 186 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8121 (p) REVERT: A 346 CYS cc_start: 0.8429 (m) cc_final: 0.7855 (p) REVERT: B 23 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.7977 (tp) REVERT: B 245 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8077 (mp) REVERT: C 220 ASN cc_start: 0.7696 (m110) cc_final: 0.7358 (m-40) REVERT: C 328 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7530 (mttm) REVERT: D 13 MET cc_start: 0.3807 (ptm) cc_final: 0.3488 (ppp) REVERT: D 68 PHE cc_start: 0.5430 (OUTLIER) cc_final: 0.4935 (m-80) REVERT: D 175 ARG cc_start: 0.6338 (ttp-170) cc_final: 0.5842 (mtm110) REVERT: D 245 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8158 (pt) REVERT: D 274 ASP cc_start: 0.8558 (p0) cc_final: 0.8105 (p0) REVERT: D 356 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8288 (mm) REVERT: D 362 GLN cc_start: 0.8302 (pt0) cc_final: 0.7859 (pm20) outliers start: 54 outliers final: 19 residues processed: 160 average time/residue: 0.5355 time to fit residues: 95.4210 Evaluate side-chains 135 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 369 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 140 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN C 31 ASN D 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.169053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099939 restraints weight = 17176.382| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.14 r_work: 0.3046 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15338 Z= 0.206 Angle : 0.554 5.834 21068 Z= 0.308 Chirality : 0.045 0.236 2358 Planarity : 0.004 0.035 2420 Dihedral : 20.771 176.128 2671 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.79 % Allowed : 22.43 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1612 helix: 1.22 (0.18), residues: 702 sheet: -0.24 (0.34), residues: 242 loop : -0.39 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 299 TYR 0.018 0.002 TYR B 244 PHE 0.021 0.001 PHE A 376 TRP 0.010 0.001 TRP B 325 HIS 0.007 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (15338) covalent geometry : angle 0.55421 / 0.31 (21068) hydrogen bonds : bond 0.04361 / 2.82 ( 697) hydrogen bonds : angle 4.32862 / 3.11 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 0.375 Fit side-chains REVERT: A 3 GLN cc_start: 0.7470 (mt0) cc_final: 0.7084 (mt0) REVERT: B 23 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.7845 (tp) REVERT: B 245 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8161 (mp) REVERT: C 86 ASN cc_start: 0.8383 (m-40) cc_final: 0.8163 (p0) REVERT: C 126 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.7046 (mm) REVERT: C 362 GLN cc_start: 0.5989 (pp30) cc_final: 0.5623 (pm20) REVERT: D 13 MET cc_start: 0.4003 (ptm) cc_final: 0.3595 (ppp) REVERT: D 68 PHE cc_start: 0.5261 (OUTLIER) cc_final: 0.4868 (m-80) REVERT: D 274 ASP cc_start: 0.8627 (p0) cc_final: 0.8130 (p0) REVERT: D 356 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8160 (mm) REVERT: D 404 GLU cc_start: 0.7812 (pt0) cc_final: 0.7484 (mm-30) outliers start: 56 outliers final: 27 residues processed: 162 average time/residue: 0.4840 time to fit residues: 87.6950 Evaluate side-chains 141 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 157 optimal weight: 0.6980 chunk 164 optimal weight: 50.0000 chunk 48 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN A 122 ASN B 67 ASN B 362 GLN D 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.170017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099926 restraints weight = 17132.257| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.18 r_work: 0.3050 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15338 Z= 0.141 Angle : 0.497 6.671 21068 Z= 0.279 Chirality : 0.043 0.230 2358 Planarity : 0.003 0.032 2420 Dihedral : 20.708 177.252 2666 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.25 % Allowed : 23.31 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1612 helix: 1.92 (0.19), residues: 699 sheet: -0.27 (0.35), residues: 238 loop : -0.18 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 299 TYR 0.013 0.001 TYR B 392 PHE 0.018 0.001 PHE A 376 TRP 0.008 0.001 TRP C 325 HIS 0.006 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (15338) covalent geometry : angle 0.49678 / 0.28 (21068) hydrogen bonds : bond 0.03686 / 2.38 ( 697) hydrogen bonds : angle 4.11221 / 2.95 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.540 Fit side-chains REVERT: A 388 ASP cc_start: 0.8226 (t70) cc_final: 0.7924 (t70) REVERT: B 23 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.7958 (tp) REVERT: C 86 ASN cc_start: 0.8383 (m-40) cc_final: 0.8172 (p0) REVERT: C 126 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.7031 (mm) REVERT: C 285 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7408 (mttm) REVERT: C 328 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7531 (mmtm) REVERT: C 362 GLN cc_start: 0.5993 (pp30) cc_final: 0.5764 (pm20) REVERT: D 121 THR cc_start: 0.7633 (p) cc_final: 0.7422 (m) REVERT: D 245 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7927 (mp) REVERT: D 274 ASP cc_start: 0.8619 (p0) cc_final: 0.8146 (p0) REVERT: D 356 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8158 (mm) REVERT: D 404 GLU cc_start: 0.7671 (pt0) cc_final: 0.7409 (mm-30) outliers start: 48 outliers final: 19 residues processed: 149 average time/residue: 0.5688 time to fit residues: 93.7344 Evaluate side-chains 132 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 136 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 68 optimal weight: 0.0870 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 ASN C 321 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101138 restraints weight = 17331.602| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.23 r_work: 0.3052 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15338 Z= 0.120 Angle : 0.486 7.625 21068 Z= 0.271 Chirality : 0.042 0.232 2358 Planarity : 0.003 0.032 2420 Dihedral : 20.605 177.333 2665 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.66 % Allowed : 22.49 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1612 helix: 2.32 (0.19), residues: 700 sheet: -0.27 (0.35), residues: 226 loop : -0.08 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 299 TYR 0.013 0.001 TYR B 392 PHE 0.017 0.001 PHE A 376 TRP 0.008 0.001 TRP B 325 HIS 0.005 0.001 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (15338) covalent geometry : angle 0.48603 / 0.27 (21068) hydrogen bonds : bond 0.03445 / 2.24 ( 697) hydrogen bonds : angle 3.95370 / 2.83 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 0.574 Fit side-chains REVERT: A 79 PRO cc_start: 0.8207 (Cg_exo) cc_final: 0.7877 (Cg_endo) REVERT: A 388 ASP cc_start: 0.8167 (t70) cc_final: 0.7860 (t70) REVERT: B 23 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.7940 (tp) REVERT: B 245 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8070 (mp) REVERT: C 86 ASN cc_start: 0.8383 (m-40) cc_final: 0.8183 (p0) REVERT: C 126 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.7019 (mm) REVERT: C 285 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7317 (mttm) REVERT: C 362 GLN cc_start: 0.5970 (pp30) cc_final: 0.5746 (pm20) REVERT: D 13 MET cc_start: 0.5911 (ppp) cc_final: 0.4055 (ptt) REVERT: D 68 PHE cc_start: 0.5575 (OUTLIER) cc_final: 0.4596 (m-80) REVERT: D 245 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7884 (mp) REVERT: D 274 ASP cc_start: 0.8562 (p0) cc_final: 0.8002 (p0) REVERT: D 356 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8116 (mm) REVERT: D 388 ASP cc_start: 0.8346 (m-30) cc_final: 0.7795 (t0) outliers start: 54 outliers final: 23 residues processed: 159 average time/residue: 0.5418 time to fit residues: 95.9554 Evaluate side-chains 139 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 132 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 49 optimal weight: 0.0870 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN B 67 ASN D 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.171317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101588 restraints weight = 17082.366| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.21 r_work: 0.3059 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15338 Z= 0.112 Angle : 0.484 7.771 21068 Z= 0.269 Chirality : 0.042 0.233 2358 Planarity : 0.003 0.032 2420 Dihedral : 20.543 177.778 2665 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.32 % Allowed : 23.04 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.21), residues: 1612 helix: 2.56 (0.19), residues: 700 sheet: -0.22 (0.36), residues: 226 loop : 0.01 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 299 TYR 0.017 0.001 TYR C 64 PHE 0.017 0.001 PHE A 376 TRP 0.008 0.001 TRP B 325 HIS 0.003 0.001 HIS D 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15338) covalent geometry : angle 0.48377 / 0.27 (21068) hydrogen bonds : bond 0.03338 / 2.16 ( 697) hydrogen bonds : angle 3.88308 / 2.78 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 108 time to evaluate : 0.587 Fit side-chains REVERT: A 79 PRO cc_start: 0.8238 (Cg_exo) cc_final: 0.7955 (Cg_endo) REVERT: A 388 ASP cc_start: 0.8126 (t70) cc_final: 0.7779 (t70) REVERT: B 23 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.7946 (tp) REVERT: B 245 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8094 (mp) REVERT: C 126 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.7031 (mm) REVERT: C 136 LYS cc_start: 0.7436 (tttp) cc_final: 0.7209 (tttp) REVERT: C 285 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7294 (mttm) REVERT: C 328 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7446 (mmtm) REVERT: C 362 GLN cc_start: 0.5966 (pp30) cc_final: 0.5762 (pm20) REVERT: D 13 MET cc_start: 0.5864 (ppp) cc_final: 0.4014 (ptt) REVERT: D 68 PHE cc_start: 0.5576 (OUTLIER) cc_final: 0.4592 (m-80) REVERT: D 245 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7884 (mp) REVERT: D 274 ASP cc_start: 0.8571 (p0) cc_final: 0.8077 (p0) REVERT: D 356 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8152 (mm) REVERT: D 388 ASP cc_start: 0.8342 (m-30) cc_final: 0.7782 (t0) outliers start: 49 outliers final: 25 residues processed: 146 average time/residue: 0.5674 time to fit residues: 91.5763 Evaluate side-chains 139 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 154 optimal weight: 0.0670 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.169790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099659 restraints weight = 17036.698| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.17 r_work: 0.3046 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15338 Z= 0.142 Angle : 0.494 6.543 21068 Z= 0.274 Chirality : 0.043 0.232 2358 Planarity : 0.003 0.032 2420 Dihedral : 20.542 177.618 2665 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.32 % Allowed : 23.37 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.21), residues: 1612 helix: 2.62 (0.19), residues: 699 sheet: -0.22 (0.36), residues: 232 loop : 0.09 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 299 TYR 0.012 0.001 TYR B 244 PHE 0.017 0.001 PHE A 376 TRP 0.009 0.001 TRP B 325 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (15338) covalent geometry : angle 0.49358 / 0.27 (21068) hydrogen bonds : bond 0.03499 / 2.28 ( 697) hydrogen bonds : angle 3.89426 / 2.80 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 0.562 Fit side-chains REVERT: A 79 PRO cc_start: 0.8249 (Cg_exo) cc_final: 0.7924 (Cg_endo) REVERT: A 317 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7562 (mmtm) REVERT: A 388 ASP cc_start: 0.8213 (t70) cc_final: 0.7890 (t70) REVERT: B 245 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8124 (mp) REVERT: C 285 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7312 (mttm) REVERT: C 362 GLN cc_start: 0.5935 (pp30) cc_final: 0.5731 (pm20) REVERT: D 13 MET cc_start: 0.5819 (ppp) cc_final: 0.3937 (ptt) REVERT: D 68 PHE cc_start: 0.5583 (OUTLIER) cc_final: 0.4599 (m-80) REVERT: D 245 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7916 (mp) REVERT: D 274 ASP cc_start: 0.8603 (p0) cc_final: 0.8120 (p0) REVERT: D 356 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8147 (mm) REVERT: D 381 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7581 (mtt90) outliers start: 49 outliers final: 23 residues processed: 145 average time/residue: 0.5629 time to fit residues: 89.7409 Evaluate side-chains 132 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 2.9990 chunk 161 optimal weight: 40.0000 chunk 35 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 111 optimal weight: 0.5980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.169178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.098929 restraints weight = 17175.703| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.18 r_work: 0.3033 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15338 Z= 0.157 Angle : 0.505 7.020 21068 Z= 0.279 Chirality : 0.043 0.231 2358 Planarity : 0.003 0.033 2420 Dihedral : 20.541 177.909 2663 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.85 % Allowed : 23.92 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.21), residues: 1612 helix: 2.53 (0.19), residues: 706 sheet: -0.23 (0.36), residues: 232 loop : 0.15 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 299 TYR 0.013 0.001 TYR B 244 PHE 0.017 0.001 PHE A 376 TRP 0.009 0.001 TRP A 325 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (15338) covalent geometry : angle 0.50537 / 0.28 (21068) hydrogen bonds : bond 0.03556 / 2.31 ( 697) hydrogen bonds : angle 3.90958 / 2.80 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.490 Fit side-chains REVERT: A 79 PRO cc_start: 0.8244 (Cg_exo) cc_final: 0.7913 (Cg_endo) REVERT: A 295 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7813 (pttt) REVERT: A 388 ASP cc_start: 0.8262 (t70) cc_final: 0.7948 (t70) REVERT: B 245 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8121 (mp) REVERT: C 126 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6981 (mm) REVERT: C 136 LYS cc_start: 0.7532 (tttp) cc_final: 0.7303 (tttp) REVERT: C 285 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7286 (mttm) REVERT: C 362 GLN cc_start: 0.5940 (pp30) cc_final: 0.5736 (pm20) REVERT: D 13 MET cc_start: 0.5872 (ppp) cc_final: 0.5338 (ppp) REVERT: D 68 PHE cc_start: 0.5598 (OUTLIER) cc_final: 0.5042 (m-80) REVERT: D 245 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7912 (mp) REVERT: D 274 ASP cc_start: 0.8643 (p0) cc_final: 0.8161 (p0) REVERT: D 356 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8147 (mm) REVERT: D 381 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7568 (mtt90) outliers start: 42 outliers final: 22 residues processed: 136 average time/residue: 0.6171 time to fit residues: 92.4211 Evaluate side-chains 134 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 12 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.169384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099168 restraints weight = 17140.411| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.17 r_work: 0.3038 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15338 Z= 0.144 Angle : 0.501 10.652 21068 Z= 0.276 Chirality : 0.042 0.230 2358 Planarity : 0.003 0.034 2420 Dihedral : 20.530 178.252 2663 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.78 % Allowed : 23.78 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.22), residues: 1612 helix: 2.58 (0.19), residues: 706 sheet: -0.28 (0.35), residues: 232 loop : 0.18 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 299 TYR 0.012 0.001 TYR B 392 PHE 0.018 0.001 PHE A 376 TRP 0.009 0.001 TRP A 325 HIS 0.003 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (15338) covalent geometry : angle 0.50097 / 0.28 (21068) hydrogen bonds : bond 0.03479 / 2.26 ( 697) hydrogen bonds : angle 3.88007 / 2.78 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.444 Fit side-chains REVERT: A 79 PRO cc_start: 0.8252 (Cg_exo) cc_final: 0.7937 (Cg_endo) REVERT: A 317 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7552 (mmtm) REVERT: A 388 ASP cc_start: 0.8259 (t70) cc_final: 0.7918 (t70) REVERT: C 126 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.7015 (mm) REVERT: C 285 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7283 (mttm) REVERT: D 13 MET cc_start: 0.5896 (ppp) cc_final: 0.5110 (ppp) REVERT: D 68 PHE cc_start: 0.5606 (OUTLIER) cc_final: 0.5024 (m-80) REVERT: D 245 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7898 (mp) REVERT: D 274 ASP cc_start: 0.8623 (p0) cc_final: 0.8130 (p0) REVERT: D 356 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8142 (mm) REVERT: D 381 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7037 (mtt90) REVERT: D 404 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7123 (mt-10) outliers start: 41 outliers final: 21 residues processed: 138 average time/residue: 0.5307 time to fit residues: 81.0213 Evaluate side-chains 132 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 104 optimal weight: 0.0670 chunk 50 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 166 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN B 67 ASN C 148 ASN D 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098732 restraints weight = 17130.835| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.17 r_work: 0.3030 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15338 Z= 0.155 Angle : 0.510 11.437 21068 Z= 0.280 Chirality : 0.043 0.239 2358 Planarity : 0.003 0.035 2420 Dihedral : 20.544 178.221 2663 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.44 % Allowed : 24.39 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.22), residues: 1612 helix: 2.56 (0.19), residues: 705 sheet: -0.32 (0.35), residues: 232 loop : 0.18 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 299 TYR 0.013 0.001 TYR B 392 PHE 0.019 0.001 PHE A 376 TRP 0.009 0.001 TRP A 325 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (15338) covalent geometry : angle 0.50965 / 0.28 (21068) hydrogen bonds : bond 0.03541 / 2.30 ( 697) hydrogen bonds : angle 3.89886 / 2.80 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.570 Fit side-chains REVERT: A 388 ASP cc_start: 0.8289 (t70) cc_final: 0.7964 (t70) REVERT: B 1 MET cc_start: 0.6861 (tpp) cc_final: 0.6523 (tpp) REVERT: C 126 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.7008 (mm) REVERT: C 285 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7297 (mttm) REVERT: D 13 MET cc_start: 0.5904 (ppp) cc_final: 0.5118 (ppp) REVERT: D 68 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.5028 (m-80) REVERT: D 245 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7903 (mp) REVERT: D 274 ASP cc_start: 0.8634 (p0) cc_final: 0.8139 (p0) REVERT: D 356 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8144 (mm) REVERT: D 381 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7042 (mtt90) REVERT: D 404 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7122 (mt-10) outliers start: 36 outliers final: 24 residues processed: 130 average time/residue: 0.5967 time to fit residues: 85.7126 Evaluate side-chains 130 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 167 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098323 restraints weight = 16989.178| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.17 r_work: 0.3022 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15338 Z= 0.178 Angle : 0.524 11.311 21068 Z= 0.287 Chirality : 0.043 0.245 2358 Planarity : 0.003 0.037 2420 Dihedral : 20.569 178.228 2663 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.44 % Allowed : 24.46 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.21), residues: 1612 helix: 2.51 (0.19), residues: 705 sheet: -0.35 (0.35), residues: 232 loop : 0.18 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 299 TYR 0.013 0.001 TYR B 244 PHE 0.020 0.001 PHE A 376 TRP 0.009 0.001 TRP A 325 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (15338) covalent geometry : angle 0.52399 / 0.29 (21068) hydrogen bonds : bond 0.03641 / 2.37 ( 697) hydrogen bonds : angle 3.91545 / 2.81 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5058.93 seconds wall clock time: 86 minutes 58.41 seconds (5218.41 seconds total)