Starting phenix.real_space_refine on Thu Aug 6 10:09:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ps5_17845/08_2026/8ps5_17845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps5_17845/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ps5_17845/08_2026/8ps5_17845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps5_17845/08_2026/8ps5_17845.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ps5_17845/08_2026/8ps5_17845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps5_17845/08_2026/8ps5_17845.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 3.56, 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: 1.07 Conformation dependent library (CDL) restraints added in 480.1 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: 1.78 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: 2.89 Time building geometry restraints manager: 1.41 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: 20345 2.35 - 4.69: 630 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: 0.01 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.690 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.920 ------------------------------------------------------------------------------- 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= 0.413 Angle : 0.966 11.734 21068 Z= 0.637 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 0.96600 / 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 : 0.559 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: 0.6386 time to fit residues: 122.8999 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 : 0.654 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.174028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106474 restraints weight = 17040.850| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.18 r_work: 0.3156 rms_B_bonded: 2.79 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: 0.8148 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15338 Z= 0.123 Angle : 0.543 7.430 21068 Z= 0.309 Chirality : 0.043 0.244 2358 Planarity : 0.005 0.039 2420 Dihedral : 20.749 176.029 2678 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.73 % Allowed : 23.04 % 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: -0.58 (0.19), residues: 1612 helix: 0.06 (0.17), residues: 696 sheet: -0.25 (0.35), residues: 228 loop : -0.75 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 299 TYR 0.015 0.001 TYR B 392 PHE 0.016 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 0.54313 / 0.31 (21068) hydrogen bonds : bond 0.04510 / 2.90 ( 697) hydrogen bonds : angle 4.79306 / 3.43 ( 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 176 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 0.541 Fit side-chains REVERT: A 1 MET cc_start: 0.3451 (tpp) cc_final: 0.3226 (tpt) REVERT: A 3 GLN cc_start: 0.7470 (mt0) cc_final: 0.7082 (mt0) REVERT: A 346 CYS cc_start: 0.8419 (m) cc_final: 0.7845 (p) REVERT: B 11 VAL cc_start: 0.7490 (t) cc_final: 0.7270 (p) REVERT: B 23 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.7977 (tp) REVERT: B 245 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8075 (mp) REVERT: C 220 ASN cc_start: 0.7715 (m110) cc_final: 0.7380 (m-40) REVERT: C 328 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7580 (mttm) REVERT: D 13 MET cc_start: 0.3808 (ptm) cc_final: 0.3489 (ppp) REVERT: D 68 PHE cc_start: 0.5435 (OUTLIER) cc_final: 0.4947 (m-80) REVERT: D 175 ARG cc_start: 0.6326 (ttp-170) cc_final: 0.5833 (mtm110) REVERT: D 245 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8079 (pt) REVERT: D 356 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8252 (mm) REVERT: D 362 GLN cc_start: 0.8297 (pt0) cc_final: 0.7855 (pm20) outliers start: 55 outliers final: 20 residues processed: 161 average time/residue: 0.5509 time to fit residues: 98.9503 Evaluate side-chains 136 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 A residue 387 ILE 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: 0.9990 chunk 86 optimal weight: 30.0000 chunk 84 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.170807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101119 restraints weight = 17250.112| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.22 r_work: 0.3028 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15338 Z= 0.175 Angle : 0.534 6.017 21068 Z= 0.298 Chirality : 0.044 0.258 2358 Planarity : 0.003 0.033 2420 Dihedral : 20.685 175.549 2671 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.52 % Allowed : 22.90 % Favored : 73.58 % 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: 1.25 (0.18), residues: 702 sheet: -0.21 (0.35), residues: 242 loop : -0.43 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 360 TYR 0.016 0.001 TYR B 244 PHE 0.019 0.001 PHE A 376 TRP 0.009 0.001 TRP B 325 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (15338) covalent geometry : angle 0.53448 / 0.30 (21068) hydrogen bonds : bond 0.04120 / 2.67 ( 697) hydrogen bonds : angle 4.33001 / 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: 52 poor density : 124 time to evaluate : 0.463 Fit side-chains REVERT: A 3 GLN cc_start: 0.7384 (mt0) cc_final: 0.7018 (mt0) REVERT: A 346 CYS cc_start: 0.8465 (m) cc_final: 0.7770 (p) REVERT: A 388 ASP cc_start: 0.8123 (t70) cc_final: 0.7909 (t70) REVERT: B 23 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.7824 (tp) REVERT: B 245 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8104 (mp) REVERT: C 86 ASN cc_start: 0.8358 (m-40) cc_final: 0.8135 (p0) REVERT: C 126 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6943 (mm) REVERT: C 362 GLN cc_start: 0.5876 (pp30) cc_final: 0.5537 (pm20) REVERT: D 13 MET cc_start: 0.3978 (ptm) cc_final: 0.3575 (ppp) REVERT: D 68 PHE cc_start: 0.5188 (OUTLIER) cc_final: 0.4820 (m-80) REVERT: D 175 ARG cc_start: 0.6164 (ttp-170) cc_final: 0.5659 (mtm110) REVERT: D 245 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7948 (mp) REVERT: D 274 ASP cc_start: 0.8549 (p0) cc_final: 0.8086 (p0) REVERT: D 356 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8137 (mm) REVERT: D 404 GLU cc_start: 0.7721 (pt0) cc_final: 0.7370 (mm-30) outliers start: 52 outliers final: 27 residues processed: 162 average time/residue: 0.4990 time to fit residues: 90.7646 Evaluate side-chains 142 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 186 THR 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 A residue 387 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 SER 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 164 optimal weight: 50.0000 chunk 48 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN A 122 ASN B 67 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 = 0.3959 r_free = 0.3959 target = 0.167735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097234 restraints weight = 17162.318| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.18 r_work: 0.3006 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15338 Z= 0.231 Angle : 0.562 5.787 21068 Z= 0.308 Chirality : 0.046 0.253 2358 Planarity : 0.004 0.036 2420 Dihedral : 20.769 175.625 2667 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.79 % Allowed : 22.36 % 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: 0.84 (0.21), residues: 1612 helix: 1.64 (0.19), residues: 701 sheet: -0.31 (0.35), residues: 226 loop : -0.19 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.017 0.002 TYR B 244 PHE 0.021 0.001 PHE A 376 TRP 0.010 0.001 TRP C 325 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 (15338) covalent geometry : angle 0.56175 / 0.31 (21068) hydrogen bonds : bond 0.04218 / 2.72 ( 697) hydrogen bonds : angle 4.24018 / 3.04 ( 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 168 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 112 time to evaluate : 0.412 Fit side-chains REVERT: A 388 ASP cc_start: 0.8269 (t70) cc_final: 0.8067 (t70) REVERT: B 23 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.7966 (tp) REVERT: B 245 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8168 (mp) REVERT: B 362 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: C 86 ASN cc_start: 0.8368 (m-40) cc_final: 0.8135 (p0) REVERT: C 126 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.7011 (mm) REVERT: C 136 LYS cc_start: 0.7528 (tttp) cc_final: 0.7285 (tttp) REVERT: C 285 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7369 (mttm) REVERT: C 362 GLN cc_start: 0.5885 (pp30) cc_final: 0.5583 (pm20) REVERT: D 121 THR cc_start: 0.7613 (p) cc_final: 0.7403 (m) REVERT: D 245 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7922 (mp) REVERT: D 274 ASP cc_start: 0.8669 (p0) cc_final: 0.8197 (p0) REVERT: D 356 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8155 (mm) REVERT: D 404 GLU cc_start: 0.7643 (pt0) cc_final: 0.7388 (mm-30) outliers start: 56 outliers final: 22 residues processed: 154 average time/residue: 0.5540 time to fit residues: 94.9171 Evaluate side-chains 138 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain B residue 3 GLN 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 362 GLN 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 223 ASN Chi-restraints excluded: chain C residue 285 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 72 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.170611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100279 restraints weight = 17159.816| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.23 r_work: 0.3019 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15338 Z= 0.116 Angle : 0.495 7.271 21068 Z= 0.275 Chirality : 0.042 0.254 2358 Planarity : 0.003 0.031 2420 Dihedral : 20.649 176.833 2665 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.52 % Allowed : 22.90 % Favored : 73.58 % 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: 1.28 (0.21), residues: 1612 helix: 2.21 (0.19), residues: 698 sheet: -0.32 (0.35), residues: 232 loop : -0.09 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 A 325 HIS 0.003 0.001 HIS D 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (15338) covalent geometry : angle 0.49493 / 0.27 (21068) hydrogen bonds : bond 0.03524 / 2.27 ( 697) hydrogen bonds : angle 4.03271 / 2.89 ( 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 166 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 114 time to evaluate : 0.580 Fit side-chains REVERT: B 23 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.7954 (tp) REVERT: B 317 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7694 (mmtp) REVERT: C 86 ASN cc_start: 0.8377 (m-40) cc_final: 0.8159 (p0) REVERT: C 126 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.7002 (mm) REVERT: C 328 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7414 (mttm) REVERT: C 362 GLN cc_start: 0.5835 (pp30) cc_final: 0.5626 (pm20) REVERT: D 13 MET cc_start: 0.5674 (ppp) cc_final: 0.4090 (ptt) REVERT: D 68 PHE cc_start: 0.5552 (OUTLIER) cc_final: 0.4710 (m-80) REVERT: D 245 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7926 (mp) REVERT: D 274 ASP cc_start: 0.8640 (p0) cc_final: 0.8176 (p0) REVERT: D 356 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8115 (mm) REVERT: D 381 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7567 (mtt90) outliers start: 52 outliers final: 17 residues processed: 152 average time/residue: 0.5784 time to fit residues: 98.0810 Evaluate side-chains 129 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 281 ILE Chi-restraints excluded: chain B residue 317 LYS 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 328 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 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: 2.9990 chunk 96 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 ASN D 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.168646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098353 restraints weight = 16853.466| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.16 r_work: 0.3020 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2008 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= 0.169 Angle : 0.520 6.153 21068 Z= 0.286 Chirality : 0.044 0.254 2358 Planarity : 0.003 0.033 2420 Dihedral : 20.633 176.386 2665 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.52 % Allowed : 22.83 % 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: 1.40 (0.21), residues: 1612 helix: 2.26 (0.19), residues: 704 sheet: -0.35 (0.35), residues: 232 loop : 0.04 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.014 0.001 TYR C 64 PHE 0.019 0.001 PHE A 376 TRP 0.009 0.001 TRP B 325 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (15338) covalent geometry : angle 0.51953 / 0.29 (21068) hydrogen bonds : bond 0.03731 / 2.40 ( 697) hydrogen bonds : angle 4.01248 / 2.88 ( 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 155 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 103 time to evaluate : 0.661 Fit side-chains REVERT: B 23 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.7989 (tp) REVERT: B 245 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 317 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7823 (mmtp) REVERT: C 86 ASN cc_start: 0.8405 (m-40) cc_final: 0.8170 (p0) REVERT: C 285 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7327 (mttm) REVERT: C 328 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7571 (mmtm) REVERT: C 362 GLN cc_start: 0.5881 (OUTLIER) cc_final: 0.5663 (pm20) REVERT: D 13 MET cc_start: 0.5780 (ppp) cc_final: 0.3974 (ptt) REVERT: D 68 PHE cc_start: 0.5590 (OUTLIER) cc_final: 0.4633 (m-80) REVERT: D 245 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7951 (mp) REVERT: D 274 ASP cc_start: 0.8642 (p0) cc_final: 0.8127 (p0) REVERT: D 356 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8148 (mm) REVERT: D 381 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7637 (mtt90) outliers start: 52 outliers final: 23 residues processed: 142 average time/residue: 0.5898 time to fit residues: 92.9468 Evaluate side-chains 136 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 A residue 387 ILE Chi-restraints excluded: chain B residue 3 GLN 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 317 LYS 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 149 THR 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 C residue 362 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.169759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099843 restraints weight = 17029.059| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.17 r_work: 0.3047 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15338 Z= 0.121 Angle : 0.487 6.905 21068 Z= 0.271 Chirality : 0.042 0.254 2358 Planarity : 0.003 0.030 2420 Dihedral : 20.549 177.345 2665 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.18 % Allowed : 23.04 % 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: 1.57 (0.21), residues: 1612 helix: 2.47 (0.19), residues: 704 sheet: -0.35 (0.35), residues: 232 loop : 0.09 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 299 TYR 0.012 0.001 TYR B 392 PHE 0.017 0.001 PHE A 376 TRP 0.008 0.001 TRP A 325 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15338) covalent geometry : angle 0.48703 / 0.27 (21068) hydrogen bonds : bond 0.03411 / 2.20 ( 697) hydrogen bonds : angle 3.90288 / 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 154 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 0.582 Fit side-chains REVERT: A 79 PRO cc_start: 0.8225 (Cg_exo) cc_final: 0.7884 (Cg_endo) REVERT: A 317 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7490 (mmtm) REVERT: B 317 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7793 (mmtp) REVERT: C 86 ASN cc_start: 0.8404 (m-40) cc_final: 0.8171 (p0) REVERT: C 126 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6986 (mm) REVERT: C 136 LYS cc_start: 0.7508 (tttp) cc_final: 0.7251 (tttp) REVERT: C 285 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7263 (mttm) REVERT: C 286 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8016 (mmtm) REVERT: C 328 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7517 (mmtm) REVERT: D 13 MET cc_start: 0.5796 (ppp) cc_final: 0.3999 (ptt) REVERT: D 68 PHE cc_start: 0.5592 (OUTLIER) cc_final: 0.4628 (m-80) REVERT: D 245 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7931 (mp) REVERT: D 274 ASP cc_start: 0.8631 (p0) cc_final: 0.8160 (p0) REVERT: D 356 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8135 (mm) REVERT: D 381 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7564 (mtt90) outliers start: 47 outliers final: 20 residues processed: 143 average time/residue: 0.6076 time to fit residues: 96.3663 Evaluate side-chains 133 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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 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 317 LYS 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 149 THR Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 328 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 8.9990 chunk 161 optimal weight: 40.0000 chunk 35 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 111 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.169896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099737 restraints weight = 16975.855| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.18 r_work: 0.3044 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15338 Z= 0.127 Angle : 0.492 8.240 21068 Z= 0.273 Chirality : 0.042 0.254 2358 Planarity : 0.003 0.030 2420 Dihedral : 20.491 177.227 2663 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.78 % Allowed : 23.51 % Favored : 73.71 % 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: 1.67 (0.21), residues: 1612 helix: 2.57 (0.19), residues: 705 sheet: -0.32 (0.35), residues: 232 loop : 0.13 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 A 325 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15338) covalent geometry : angle 0.49164 / 0.27 (21068) hydrogen bonds : bond 0.03392 / 2.20 ( 697) hydrogen bonds : angle 3.89091 / 2.79 ( 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 145 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.571 Fit side-chains REVERT: A 79 PRO cc_start: 0.8208 (Cg_exo) cc_final: 0.7873 (Cg_endo) REVERT: B 245 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8105 (mp) REVERT: B 317 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7833 (mmtp) REVERT: C 86 ASN cc_start: 0.8402 (m-40) cc_final: 0.8170 (p0) REVERT: C 126 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6968 (mm) REVERT: C 136 LYS cc_start: 0.7492 (tttp) cc_final: 0.7212 (tttp) REVERT: C 285 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7267 (mttm) REVERT: D 13 MET cc_start: 0.5876 (ppp) cc_final: 0.5111 (ppp) REVERT: D 68 PHE cc_start: 0.5562 (OUTLIER) cc_final: 0.5015 (m-80) REVERT: D 245 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7933 (mp) REVERT: D 274 ASP cc_start: 0.8599 (p0) cc_final: 0.8116 (p0) REVERT: D 356 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8107 (mm) REVERT: D 381 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7572 (mtt90) outliers start: 41 outliers final: 20 residues processed: 134 average time/residue: 0.6230 time to fit residues: 92.5792 Evaluate side-chains 129 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 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 317 LYS 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 149 THR 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 369 THR Chi-restraints excluded: chain D residue 381 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 12 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 120 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.169671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099403 restraints weight = 16946.113| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.18 r_work: 0.3039 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15338 Z= 0.134 Angle : 0.499 11.278 21068 Z= 0.276 Chirality : 0.042 0.253 2358 Planarity : 0.003 0.031 2420 Dihedral : 20.481 177.443 2663 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.37 % Allowed : 23.92 % Favored : 73.71 % 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: 2.60 (0.19), residues: 705 sheet: -0.33 (0.35), residues: 232 loop : 0.18 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.012 0.001 TYR B 392 PHE 0.018 0.001 PHE A 376 TRP 0.008 0.001 TRP A 325 HIS 0.003 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15338) covalent geometry : angle 0.49865 / 0.28 (21068) hydrogen bonds : bond 0.03417 / 2.22 ( 697) hydrogen bonds : angle 3.87677 / 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 140 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.580 Fit side-chains REVERT: A 79 PRO cc_start: 0.8212 (Cg_exo) cc_final: 0.7901 (Cg_endo) REVERT: A 295 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7876 (pttt) REVERT: A 317 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7533 (mmtm) REVERT: B 245 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 317 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7833 (mmtp) REVERT: C 126 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6993 (mm) REVERT: C 136 LYS cc_start: 0.7514 (tttp) cc_final: 0.7300 (tttp) REVERT: C 285 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7294 (mttm) REVERT: D 13 MET cc_start: 0.5849 (ppp) cc_final: 0.5071 (ppp) REVERT: D 68 PHE cc_start: 0.5594 (OUTLIER) cc_final: 0.5033 (m-80) REVERT: D 245 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7929 (mp) REVERT: D 274 ASP cc_start: 0.8595 (p0) cc_final: 0.8055 (p0) REVERT: D 356 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8118 (mm) REVERT: D 381 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7566 (mtt90) REVERT: D 404 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7105 (mt-10) outliers start: 35 outliers final: 17 residues processed: 132 average time/residue: 0.6249 time to fit residues: 91.2630 Evaluate side-chains 129 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 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 317 LYS 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 149 THR 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 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: 1.9990 chunk 104 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 166 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.168929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098582 restraints weight = 16973.196| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.16 r_work: 0.3026 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15338 Z= 0.165 Angle : 0.523 12.102 21068 Z= 0.286 Chirality : 0.043 0.251 2358 Planarity : 0.003 0.033 2420 Dihedral : 20.523 177.337 2663 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.17 % Allowed : 24.32 % Favored : 73.51 % 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: 1.67 (0.22), residues: 1612 helix: 2.53 (0.19), residues: 705 sheet: -0.36 (0.35), residues: 232 loop : 0.20 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.013 0.001 TYR B 244 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 0.00397 / 0.17 (15338) covalent geometry : angle 0.52337 / 0.29 (21068) hydrogen bonds : bond 0.03593 / 2.33 ( 697) hydrogen bonds : angle 3.92085 / 2.82 ( 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 135 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.541 Fit side-chains REVERT: A 295 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7899 (pttt) REVERT: A 317 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7571 (mmtm) REVERT: B 73 ASN cc_start: 0.8160 (t0) cc_final: 0.7845 (t0) REVERT: B 317 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7862 (mmtp) REVERT: C 126 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.7014 (mm) REVERT: C 136 LYS cc_start: 0.7522 (tttp) cc_final: 0.7305 (tttp) REVERT: C 285 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7285 (mttm) REVERT: D 13 MET cc_start: 0.5859 (ppp) cc_final: 0.5106 (ppp) REVERT: D 68 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.5074 (m-80) REVERT: D 245 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7936 (mp) REVERT: D 274 ASP cc_start: 0.8608 (p0) cc_final: 0.8131 (p0) REVERT: D 356 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8132 (mm) REVERT: D 381 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7567 (mtt90) REVERT: D 404 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7111 (mt-10) outliers start: 32 outliers final: 19 residues processed: 128 average time/residue: 0.6269 time to fit residues: 88.8707 Evaluate side-chains 131 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 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 317 LYS 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 149 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 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: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.169620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099197 restraints weight = 16966.425| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.17 r_work: 0.3037 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15338 Z= 0.129 Angle : 0.504 11.337 21068 Z= 0.278 Chirality : 0.042 0.251 2358 Planarity : 0.003 0.034 2420 Dihedral : 20.502 177.728 2663 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.10 % Allowed : 24.25 % 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: 1.73 (0.22), residues: 1612 helix: 2.62 (0.19), residues: 705 sheet: -0.37 (0.35), residues: 232 loop : 0.19 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 50 TYR 0.013 0.001 TYR B 392 PHE 0.018 0.001 PHE A 376 TRP 0.008 0.001 TRP A 325 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (15338) covalent geometry : angle 0.50382 / 0.28 (21068) hydrogen bonds : bond 0.03419 / 2.22 ( 697) hydrogen bonds : angle 3.88162 / 2.79 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5706.96 seconds wall clock time: 98 minutes 0.78 seconds (5880.78 seconds total)