Starting phenix.real_space_refine on Sat Aug 23 21:12:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ps5_17845/08_2025/8ps5_17845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps5_17845/08_2025/8ps5_17845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ps5_17845/08_2025/8ps5_17845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps5_17845/08_2025/8ps5_17845.map" model { file = "/net/cci-nas-00/data/ceres_data/8ps5_17845/08_2025/8ps5_17845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps5_17845/08_2025/8ps5_17845.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 78 5.49 5 S 40 5.16 5 C 9276 2.51 5 N 2550 2.21 5 O 2942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 4.29, per 1000 atoms: 0.29 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: 1.33 Conformation dependent library (CDL) restraints added in 684.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 45.6% alpha, 14.9% beta 38 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 2.21 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: 3.11 Time building geometry restraints manager: 1.79 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=" 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=" 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 bond pdb=" N ILE D 91 " pdb=" CA ILE D 91 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.39e+00 bond pdb=" N VAL D 89 " pdb=" CA VAL D 89 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.19e-02 7.06e+03 9.37e+00 ... (remaining 15333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 20415 2.35 - 4.69: 560 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: 2262 0.132 - 0.263: 92 0.263 - 0.395: 2 0.395 - 0.526: 1 0.526 - 0.658: 1 Chirality restraints: 2358 Sorted by residual: chirality pdb=" CB ILE B 245 " pdb=" CA ILE B 245 " pdb=" CG1 ILE B 245 " pdb=" CG2 ILE B 245 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA ASP B 169 " pdb=" N ASP B 169 " pdb=" C ASP B 169 " pdb=" CB ASP B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CA ILE D 234 " pdb=" N ILE D 234 " pdb=" C ILE D 234 " pdb=" CB ILE D 234 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2355 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 40 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C ARG C 40 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG C 40 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C 41 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 121 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C THR B 121 " -0.048 2.00e-02 2.50e+03 pdb=" O THR B 121 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 122 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 121 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C THR A 121 " 0.043 2.00e-02 2.50e+03 pdb=" O THR A 121 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 122 " -0.014 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1723 2.76 - 3.29: 13082 3.29 - 3.83: 25806 3.83 - 4.36: 31051 4.36 - 4.90: 51078 Nonbonded interactions: 122740 Sorted by model distance: nonbonded pdb=" OD2 ASP D 255 " pdb=" OG1 THR D 264 " model vdw 2.221 3.040 nonbonded pdb=" O ARG D 113 " pdb=" CD1 LEU D 117 " model vdw 2.226 3.460 nonbonded pdb=" NZ LYS B 263 " pdb=" OP2 DG F 22 " model vdw 2.286 3.120 nonbonded pdb=" O SER D 350 " pdb=" OG SER D 350 " model vdw 2.316 3.040 nonbonded pdb=" OE1 GLU A 330 " pdb=" OH TYR C 257 " model vdw 2.338 3.040 ... (remaining 122735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 16 or resid 21 through 408)) selection = (chain 'B' and (resid 1 through 16 or resid 21 through 408)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.030 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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= 0.326 Angle : 0.936 11.734 21068 Z= 0.575 Chirality : 0.058 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 aren 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 covalent geometry : bond 0.00571 (15338) covalent geometry : angle 0.93607 (21068) hydrogen bonds : bond 0.19076 ( 697) hydrogen bonds : angle 7.73830 ( 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 : 0.587 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: 0.7656 (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: 0.6857 time to fit residues: 131.4658 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 : 0.590 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 143 GLN B 45 GLN B 362 GLN C 31 ASN C 43 ASN C 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.174136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105543 restraints weight = 17035.993| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.23 r_work: 0.3111 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15338 Z= 0.116 Angle : 0.495 7.572 21068 Z= 0.281 Chirality : 0.040 0.214 2358 Planarity : 0.004 0.039 2420 Dihedral : 20.300 176.902 2678 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.86 % Allowed : 22.90 % 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 aren not related in a simple way. whole: -0.46 (0.19), residues: 1612 helix: 0.17 (0.17), residues: 696 sheet: -0.18 (0.34), residues: 241 loop : -0.71 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 299 TYR 0.012 0.001 TYR B 392 PHE 0.016 0.001 PHE A 376 TRP 0.007 0.001 TRP D 27 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00250 (15338) covalent geometry : angle 0.49489 (21068) hydrogen bonds : bond 0.03787 ( 697) hydrogen bonds : angle 4.51140 ( 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 180 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 123 time to evaluate : 0.614 Fit side-chains REVERT: A 1 MET cc_start: 0.3246 (tpp) cc_final: 0.3041 (tpt) REVERT: A 3 GLN cc_start: 0.7313 (mt0) cc_final: 0.6980 (mt0) REVERT: A 346 CYS cc_start: 0.8374 (m) cc_final: 0.7728 (p) REVERT: B 23 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7829 (tp) REVERT: B 245 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7953 (mp) REVERT: B 317 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7690 (mmtm) REVERT: C 136 LYS cc_start: 0.7351 (tttp) cc_final: 0.7116 (tttp) REVERT: C 220 ASN cc_start: 0.7515 (m110) cc_final: 0.7125 (m-40) REVERT: C 394 ASP cc_start: 0.7524 (t0) cc_final: 0.7267 (t0) REVERT: D 13 MET cc_start: 0.3824 (ptm) cc_final: 0.3471 (ppp) REVERT: D 68 PHE cc_start: 0.5278 (OUTLIER) cc_final: 0.4857 (m-80) REVERT: D 116 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7220 (mptm) REVERT: D 175 ARG cc_start: 0.6053 (ttp-170) cc_final: 0.5575 (mtm110) REVERT: D 245 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7947 (pt) REVERT: D 274 ASP cc_start: 0.8345 (p0) cc_final: 0.7788 (p0) REVERT: D 356 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8148 (mm) REVERT: D 362 GLN cc_start: 0.8283 (pt0) cc_final: 0.7783 (pm20) REVERT: D 404 GLU cc_start: 0.7687 (pt0) cc_final: 0.7352 (mm-30) outliers start: 57 outliers final: 19 residues processed: 164 average time/residue: 0.6204 time to fit residues: 112.4084 Evaluate side-chains 139 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 149 THR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 140 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 122 ASN B 51 ASN B 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.167417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096838 restraints weight = 17296.331| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.19 r_work: 0.3002 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15338 Z= 0.242 Angle : 0.571 6.586 21068 Z= 0.314 Chirality : 0.045 0.246 2358 Planarity : 0.004 0.032 2420 Dihedral : 20.469 175.952 2669 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.66 % Allowed : 22.63 % 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 aren not related in a simple way. whole: 0.48 (0.20), residues: 1612 helix: 1.19 (0.18), residues: 706 sheet: -0.26 (0.35), residues: 226 loop : -0.30 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.019 0.002 TYR B 244 PHE 0.020 0.002 PHE A 376 TRP 0.010 0.002 TRP A 325 HIS 0.008 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00597 (15338) covalent geometry : angle 0.57133 (21068) hydrogen bonds : bond 0.04334 ( 697) hydrogen bonds : angle 4.25605 ( 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 170 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 0.552 Fit side-chains REVERT: B 23 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.7973 (tp) REVERT: C 126 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.7047 (mm) REVERT: C 285 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7348 (mttm) REVERT: D 245 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7918 (mp) REVERT: D 274 ASP cc_start: 0.8740 (p0) cc_final: 0.8324 (p0) REVERT: D 356 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8105 (mm) REVERT: D 381 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7583 (mtt90) outliers start: 54 outliers final: 18 residues processed: 157 average time/residue: 0.5168 time to fit residues: 90.1190 Evaluate side-chains 135 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 86 ASN 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 279 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 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 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 381 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 84 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 164 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN B 51 ASN B 67 ASN C 321 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100968 restraints weight = 17277.309| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.22 r_work: 0.3051 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15338 Z= 0.118 Angle : 0.473 6.583 21068 Z= 0.266 Chirality : 0.041 0.184 2358 Planarity : 0.003 0.033 2420 Dihedral : 20.201 177.687 2665 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.91 % Allowed : 23.92 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.21), residues: 1612 helix: 2.05 (0.19), residues: 704 sheet: -0.27 (0.35), residues: 226 loop : -0.16 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 B 325 HIS 0.006 0.001 HIS D 120 Details of bonding type rmsd covalent geometry : bond 0.00270 (15338) covalent geometry : angle 0.47342 (21068) hydrogen bonds : bond 0.03246 ( 697) hydrogen bonds : angle 3.95950 ( 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 163 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 0.396 Fit side-chains REVERT: A 79 PRO cc_start: 0.8202 (Cg_exo) cc_final: 0.7883 (Cg_endo) REVERT: A 388 ASP cc_start: 0.8211 (t70) cc_final: 0.7898 (t70) REVERT: B 23 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.7957 (tp) REVERT: B 362 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: C 136 LYS cc_start: 0.7520 (tttp) cc_final: 0.7275 (tttp) REVERT: D 13 MET cc_start: 0.5822 (ppp) cc_final: 0.3863 (ptt) REVERT: D 68 PHE cc_start: 0.5563 (OUTLIER) cc_final: 0.4573 (m-80) REVERT: D 245 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7876 (mp) REVERT: D 274 ASP cc_start: 0.8617 (p0) cc_final: 0.8071 (p0) REVERT: D 356 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8091 (mm) REVERT: D 381 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6976 (mtt90) outliers start: 43 outliers final: 14 residues processed: 153 average time/residue: 0.5953 time to fit residues: 100.5360 Evaluate side-chains 125 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 282 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 14 THR 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 369 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 151 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 143 optimal weight: 0.0020 chunk 136 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 68 optimal weight: 0.1980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4003 r_free = 0.4003 target = 0.172214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102597 restraints weight = 17207.299| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.23 r_work: 0.3072 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15338 Z= 0.107 Angle : 0.461 9.034 21068 Z= 0.257 Chirality : 0.040 0.164 2358 Planarity : 0.003 0.032 2420 Dihedral : 19.931 177.546 2665 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.91 % Allowed : 24.32 % Favored : 72.76 % 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 aren not related in a simple way. whole: 1.58 (0.21), residues: 1612 helix: 2.53 (0.19), residues: 705 sheet: -0.27 (0.35), residues: 226 loop : -0.01 (0.24), residues: 681 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 0.014 0.001 PHE A 376 TRP 0.008 0.001 TRP D 325 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00237 (15338) covalent geometry : angle 0.46138 (21068) hydrogen bonds : bond 0.02971 ( 697) hydrogen bonds : angle 3.77515 ( 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 151 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.699 Fit side-chains REVERT: A 79 PRO cc_start: 0.8241 (Cg_exo) cc_final: 0.7937 (Cg_endo) REVERT: A 388 ASP cc_start: 0.8149 (t70) cc_final: 0.7786 (t70) REVERT: B 362 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.6869 (pm20) REVERT: C 126 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.7002 (mm) REVERT: C 136 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7212 (tttp) REVERT: C 285 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7252 (mttm) REVERT: D 13 MET cc_start: 0.5805 (ppp) cc_final: 0.3937 (ptt) REVERT: D 68 PHE cc_start: 0.5592 (OUTLIER) cc_final: 0.4546 (m-80) REVERT: D 245 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7869 (mp) REVERT: D 356 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8050 (mm) REVERT: D 388 ASP cc_start: 0.8375 (m-30) cc_final: 0.7838 (t0) outliers start: 43 outliers final: 18 residues processed: 141 average time/residue: 0.6136 time to fit residues: 95.7500 Evaluate side-chains 128 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 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 362 GLN 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 136 LYS Chi-restraints excluded: chain C residue 285 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 132 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 130 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 chunk 147 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4004 r_free = 0.4004 target = 0.172235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102569 restraints weight = 16957.684| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.22 r_work: 0.3071 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15338 Z= 0.110 Angle : 0.459 6.039 21068 Z= 0.256 Chirality : 0.040 0.163 2358 Planarity : 0.003 0.032 2420 Dihedral : 19.822 177.984 2663 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.78 % Allowed : 24.46 % Favored : 72.76 % 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 aren not related in a simple way. whole: 1.80 (0.21), residues: 1612 helix: 2.73 (0.19), residues: 706 sheet: -0.25 (0.35), residues: 226 loop : 0.10 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 299 TYR 0.014 0.001 TYR C 181 PHE 0.015 0.001 PHE A 376 TRP 0.008 0.001 TRP A 325 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00247 (15338) covalent geometry : angle 0.45949 (21068) hydrogen bonds : bond 0.02985 ( 697) hydrogen bonds : angle 3.71372 ( 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 150 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.583 Fit side-chains REVERT: A 79 PRO cc_start: 0.8229 (Cg_exo) cc_final: 0.7948 (Cg_endo) REVERT: A 388 ASP cc_start: 0.8165 (t70) cc_final: 0.7834 (t70) REVERT: B 1 MET cc_start: 0.7095 (tpp) cc_final: 0.6722 (tpp) REVERT: B 362 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: C 136 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7196 (tttp) REVERT: C 285 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7203 (mttm) REVERT: D 13 MET cc_start: 0.5720 (ppp) cc_final: 0.4928 (ppp) REVERT: D 68 PHE cc_start: 0.5573 (OUTLIER) cc_final: 0.4941 (m-80) REVERT: D 274 ASP cc_start: 0.8548 (p0) cc_final: 0.8124 (p0) REVERT: D 356 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8058 (mm) REVERT: D 388 ASP cc_start: 0.8358 (m-30) cc_final: 0.7812 (t0) outliers start: 41 outliers final: 19 residues processed: 139 average time/residue: 0.5449 time to fit residues: 83.8253 Evaluate side-chains 127 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 209 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 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 362 GLN Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 222 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 53 optimal weight: 0.0370 chunk 77 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 154 optimal weight: 0.0470 chunk 133 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4009 r_free = 0.4009 target = 0.172685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103065 restraints weight = 17016.342| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.22 r_work: 0.3084 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15338 Z= 0.105 Angle : 0.454 6.709 21068 Z= 0.254 Chirality : 0.040 0.161 2358 Planarity : 0.003 0.031 2420 Dihedral : 19.748 178.151 2661 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.57 % Allowed : 24.73 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.22), residues: 1612 helix: 2.87 (0.19), residues: 706 sheet: -0.19 (0.37), residues: 216 loop : 0.19 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 299 TYR 0.018 0.001 TYR C 64 PHE 0.018 0.001 PHE A 376 TRP 0.007 0.001 TRP D 325 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00232 (15338) covalent geometry : angle 0.45407 (21068) hydrogen bonds : bond 0.02928 ( 697) hydrogen bonds : angle 3.67883 ( 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 145 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.369 Fit side-chains REVERT: A 79 PRO cc_start: 0.8233 (Cg_exo) cc_final: 0.7939 (Cg_endo) REVERT: A 388 ASP cc_start: 0.8084 (t70) cc_final: 0.7701 (t70) REVERT: B 1 MET cc_start: 0.7188 (tpp) cc_final: 0.6832 (tpp) REVERT: B 88 ASP cc_start: 0.8170 (m-30) cc_final: 0.7912 (m-30) REVERT: B 245 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.8025 (mp) REVERT: C 136 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7236 (tttp) REVERT: C 285 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7164 (mttm) REVERT: D 13 MET cc_start: 0.5665 (ppp) cc_final: 0.4864 (ppp) REVERT: D 68 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: D 274 ASP cc_start: 0.8515 (p0) cc_final: 0.8064 (p0) REVERT: D 388 ASP cc_start: 0.8346 (m-30) cc_final: 0.7790 (t0) REVERT: D 404 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7070 (mt-10) outliers start: 38 outliers final: 19 residues processed: 136 average time/residue: 0.5885 time to fit residues: 88.2293 Evaluate side-chains 126 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 282 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR 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 363 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 285 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 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: 3.9990 chunk 161 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3988 r_free = 0.3988 target = 0.170146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100091 restraints weight = 17007.421| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.17 r_work: 0.3053 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15338 Z= 0.144 Angle : 0.481 7.417 21068 Z= 0.267 Chirality : 0.041 0.193 2358 Planarity : 0.003 0.030 2420 Dihedral : 19.856 178.254 2661 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.51 % Allowed : 24.73 % Favored : 72.76 % 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 aren not related in a simple way. whole: 1.86 (0.21), residues: 1612 helix: 2.76 (0.19), residues: 707 sheet: -0.33 (0.35), residues: 232 loop : 0.22 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.016 0.001 TYR C 181 PHE 0.020 0.001 PHE A 376 TRP 0.009 0.001 TRP A 325 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00345 (15338) covalent geometry : angle 0.48076 (21068) hydrogen bonds : bond 0.03298 ( 697) hydrogen bonds : angle 3.75894 ( 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 143 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.575 Fit side-chains REVERT: A 79 PRO cc_start: 0.8284 (Cg_exo) cc_final: 0.7982 (Cg_endo) REVERT: A 388 ASP cc_start: 0.8279 (t70) cc_final: 0.7892 (t70) REVERT: B 1 MET cc_start: 0.7348 (tpp) cc_final: 0.6999 (tpp) REVERT: C 136 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7296 (tttp) REVERT: C 285 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7194 (mttm) REVERT: C 286 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8247 (mttp) REVERT: D 13 MET cc_start: 0.5672 (ppp) cc_final: 0.4884 (ppp) REVERT: D 68 PHE cc_start: 0.5618 (OUTLIER) cc_final: 0.4993 (m-80) REVERT: D 98 GLU cc_start: 0.6243 (tt0) cc_final: 0.6031 (mt-10) REVERT: D 274 ASP cc_start: 0.8587 (p0) cc_final: 0.8161 (p0) REVERT: D 356 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8116 (mm) REVERT: D 404 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7120 (mt-10) outliers start: 37 outliers final: 20 residues processed: 135 average time/residue: 0.5294 time to fit residues: 78.6760 Evaluate side-chains 127 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 282 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 286 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 356 ILE Chi-restraints excluded: chain D residue 363 ILE 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: 6.9990 chunk 82 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 118 optimal weight: 0.0670 chunk 120 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN B 51 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 = 0.3981 r_free = 0.3981 target = 0.169489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099122 restraints weight = 16984.609| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.17 r_work: 0.3033 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15338 Z= 0.156 Angle : 0.498 12.757 21068 Z= 0.273 Chirality : 0.042 0.228 2358 Planarity : 0.003 0.030 2420 Dihedral : 19.929 178.487 2661 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.10 % Allowed : 24.93 % Favored : 72.97 % 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 aren not related in a simple way. whole: 1.82 (0.21), residues: 1612 helix: 2.70 (0.19), residues: 705 sheet: -0.36 (0.35), residues: 232 loop : 0.25 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.015 0.001 TYR C 181 PHE 0.021 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 covalent geometry : bond 0.00377 (15338) covalent geometry : angle 0.49788 (21068) hydrogen bonds : bond 0.03377 ( 697) hydrogen bonds : angle 3.79735 ( 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 136 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.454 Fit side-chains REVERT: A 388 ASP cc_start: 0.8338 (t70) cc_final: 0.7910 (t70) REVERT: B 1 MET cc_start: 0.7412 (tpp) cc_final: 0.7067 (tpp) REVERT: C 136 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7296 (tttp) REVERT: C 285 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7211 (mttm) REVERT: C 286 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8305 (mttp) REVERT: D 13 MET cc_start: 0.5694 (ppp) cc_final: 0.4910 (ppp) REVERT: D 68 PHE cc_start: 0.5613 (OUTLIER) cc_final: 0.5030 (m-80) REVERT: D 98 GLU cc_start: 0.6191 (tt0) cc_final: 0.5990 (mt-10) REVERT: D 274 ASP cc_start: 0.8577 (p0) cc_final: 0.8182 (p0) REVERT: D 356 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8147 (mm) REVERT: D 381 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7070 (mtt90) REVERT: D 404 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7099 (mt-10) outliers start: 31 outliers final: 17 residues processed: 129 average time/residue: 0.5685 time to fit residues: 80.7363 Evaluate side-chains 126 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 286 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 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: 2.9990 chunk 104 optimal weight: 0.0070 chunk 50 optimal weight: 0.7980 chunk 125 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 67 ASN D 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.171112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101007 restraints weight = 16976.916| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.17 r_work: 0.3068 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15338 Z= 0.118 Angle : 0.482 11.588 21068 Z= 0.266 Chirality : 0.041 0.191 2358 Planarity : 0.003 0.068 2420 Dihedral : 19.808 178.616 2661 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.63 % Allowed : 25.41 % Favored : 72.97 % 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 aren not related in a simple way. whole: 1.97 (0.22), residues: 1612 helix: 2.86 (0.19), residues: 705 sheet: -0.31 (0.36), residues: 216 loop : 0.26 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 87 TYR 0.016 0.001 TYR C 181 PHE 0.017 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 covalent geometry : bond 0.00271 (15338) covalent geometry : angle 0.48210 (21068) hydrogen bonds : bond 0.03060 ( 697) hydrogen bonds : angle 3.71548 ( 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 132 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.572 Fit side-chains REVERT: A 79 PRO cc_start: 0.8254 (Cg_exo) cc_final: 0.7930 (Cg_endo) REVERT: A 98 GLU cc_start: 0.7408 (tt0) cc_final: 0.6545 (pt0) REVERT: A 388 ASP cc_start: 0.8266 (t70) cc_final: 0.7826 (t70) REVERT: B 1 MET cc_start: 0.7433 (tpp) cc_final: 0.7115 (tpp) REVERT: C 136 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7293 (tttp) REVERT: C 285 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7209 (mttm) REVERT: C 286 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8253 (mttp) REVERT: D 13 MET cc_start: 0.5736 (ppp) cc_final: 0.4958 (ppp) REVERT: D 68 PHE cc_start: 0.5641 (OUTLIER) cc_final: 0.5012 (m-80) REVERT: D 274 ASP cc_start: 0.8601 (p0) cc_final: 0.8166 (p0) REVERT: D 356 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8094 (mm) REVERT: D 381 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7487 (mtt90) REVERT: D 404 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7105 (mt-10) outliers start: 24 outliers final: 16 residues processed: 126 average time/residue: 0.5272 time to fit residues: 73.5679 Evaluate side-chains 124 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 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 363 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 286 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 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: 0.8980 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 48 optimal weight: 0.0030 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 167 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN B 51 ASN B 67 ASN C 148 ASN D 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.172587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102662 restraints weight = 17040.670| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.21 r_work: 0.3079 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15338 Z= 0.106 Angle : 0.471 11.220 21068 Z= 0.261 Chirality : 0.040 0.168 2358 Planarity : 0.003 0.083 2420 Dihedral : 19.720 178.824 2661 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 25.27 % Favored : 72.76 % 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 aren not related in a simple way. whole: 2.05 (0.22), residues: 1612 helix: 2.97 (0.19), residues: 705 sheet: -0.30 (0.36), residues: 216 loop : 0.27 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 87 TYR 0.019 0.001 TYR C 181 PHE 0.017 0.001 PHE A 376 TRP 0.008 0.001 TRP D 325 HIS 0.002 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00236 (15338) covalent geometry : angle 0.47113 (21068) hydrogen bonds : bond 0.02924 ( 697) hydrogen bonds : angle 3.64207 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5327.37 seconds wall clock time: 91 minutes 33.25 seconds (5493.25 seconds total)