Starting phenix.real_space_refine on Sat Aug 23 15:47:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9y_37385/08_2025/8w9y_37385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9y_37385/08_2025/8w9y_37385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w9y_37385/08_2025/8w9y_37385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9y_37385/08_2025/8w9y_37385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w9y_37385/08_2025/8w9y_37385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9y_37385/08_2025/8w9y_37385.map" } resolution = 3.5 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= 0.002 sd= 0.074 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 8790 2.51 5 N 2124 2.21 5 O 2124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 13152 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "B" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "C" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "D" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Time building chain proxies: 3.15, per 1000 atoms: 0.24 Number of scatterers: 13152 At special positions: 0 Unit cell: (105.6, 160.6, 79.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 2124 8.00 N 2124 7.00 C 8790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 293 " distance=2.04 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 623.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 61.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 148 through 175 removed outlier: 3.967A pdb=" N THR A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 154 " --> pdb=" O TRP A 150 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 221 removed outlier: 4.058A pdb=" N MET A 203 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 250 removed outlier: 3.599A pdb=" N LEU A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 removed outlier: 3.959A pdb=" N LYS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS A 274 " --> pdb=" O TRP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 322 through 341 Processing helix chain 'A' and resid 345 through 370 Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.538A pdb=" N GLN A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 375' Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'B' and resid 150 through 174 removed outlier: 3.696A pdb=" N HIS B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 221 removed outlier: 3.980A pdb=" N MET B 203 " --> pdb=" O TRP B 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 250 removed outlier: 3.503A pdb=" N LEU B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 Processing helix chain 'B' and resid 299 through 315 removed outlier: 4.076A pdb=" N VAL B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 removed outlier: 3.699A pdb=" N LEU B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 370 removed outlier: 3.752A pdb=" N VAL B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'C' and resid 148 through 175 removed outlier: 3.791A pdb=" N THR C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 153 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 154 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU C 175 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 221 removed outlier: 4.214A pdb=" N MET C 203 " --> pdb=" O TRP C 199 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 250 removed outlier: 3.925A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.530A pdb=" N HIS C 274 " --> pdb=" O TRP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.744A pdb=" N VAL C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR C 315 " --> pdb=" O PHE C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 341 removed outlier: 3.506A pdb=" N ILE C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 369 removed outlier: 3.755A pdb=" N VAL C 349 " --> pdb=" O TYR C 345 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE C 355 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 4.006A pdb=" N SER C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.999A pdb=" N PHE C 388 " --> pdb=" O MET C 384 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 389' Processing helix chain 'D' and resid 150 through 177 removed outlier: 3.945A pdb=" N LEU D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG D 176 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 221 removed outlier: 3.712A pdb=" N MET D 203 " --> pdb=" O TRP D 199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 250 removed outlier: 3.622A pdb=" N LEU D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 Processing helix chain 'D' and resid 299 through 315 removed outlier: 3.919A pdb=" N VAL D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 341 removed outlier: 3.566A pdb=" N LEU D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 370 removed outlier: 3.616A pdb=" N ILE D 351 " --> pdb=" O ILE D 347 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.753A pdb=" N GLN D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 375' Processing helix chain 'E' and resid 150 through 175 removed outlier: 3.813A pdb=" N LEU E 154 " --> pdb=" O TRP E 150 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE E 160 " --> pdb=" O CYS E 156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 172 " --> pdb=" O PHE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 221 removed outlier: 3.550A pdb=" N MET E 203 " --> pdb=" O TRP E 199 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 250 removed outlier: 3.578A pdb=" N LEU E 228 " --> pdb=" O HIS E 224 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 281 removed outlier: 3.530A pdb=" N HIS E 274 " --> pdb=" O TRP E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 315 removed outlier: 3.905A pdb=" N VAL E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 341 Processing helix chain 'E' and resid 345 through 370 removed outlier: 3.748A pdb=" N ILE E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 389 removed outlier: 4.101A pdb=" N PHE E 388 " --> pdb=" O MET E 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 175 removed outlier: 3.630A pdb=" N GLU F 175 " --> pdb=" O VAL F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 194 removed outlier: 3.684A pdb=" N SER F 193 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL F 194 " --> pdb=" O PHE F 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 189 through 194' Processing helix chain 'F' and resid 199 through 222 removed outlier: 3.992A pdb=" N MET F 203 " --> pdb=" O TRP F 199 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU F 205 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 250 removed outlier: 3.699A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 230 " --> pdb=" O SER F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 281 Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.978A pdb=" N VAL F 303 " --> pdb=" O SER F 299 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL F 312 " --> pdb=" O LEU F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 341 Processing helix chain 'F' and resid 345 through 370 removed outlier: 3.807A pdb=" N VAL F 349 " --> pdb=" O TYR F 345 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 355 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 375 removed outlier: 3.984A pdb=" N SER F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 389 removed outlier: 4.035A pdb=" N PHE F 388 " --> pdb=" O MET F 384 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1827 1.32 - 1.44: 4474 1.44 - 1.57: 7150 1.57 - 1.69: 7 1.69 - 1.82: 174 Bond restraints: 13632 Sorted by residual: bond pdb=" CB PRO E 198 " pdb=" CG PRO E 198 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 1.00e+01 bond pdb=" C PRO C 255 " pdb=" O PRO C 255 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.30e-02 5.92e+03 9.67e+00 bond pdb=" CB PRO C 178 " pdb=" CG PRO C 178 " ideal model delta sigma weight residual 1.492 1.642 -0.150 5.00e-02 4.00e+02 8.98e+00 bond pdb=" CA SER C 253 " pdb=" CB SER C 253 " ideal model delta sigma weight residual 1.532 1.481 0.051 1.74e-02 3.30e+03 8.48e+00 bond pdb=" CB PRO C 185 " pdb=" CG PRO C 185 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.64e+00 ... (remaining 13627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 18381 3.03 - 6.05: 174 6.05 - 9.08: 22 9.08 - 12.10: 9 12.10 - 15.13: 2 Bond angle restraints: 18588 Sorted by residual: angle pdb=" CA PRO C 185 " pdb=" N PRO C 185 " pdb=" CD PRO C 185 " ideal model delta sigma weight residual 112.00 100.03 11.97 1.40e+00 5.10e-01 7.31e+01 angle pdb=" CA PRO C 178 " pdb=" N PRO C 178 " pdb=" CD PRO C 178 " ideal model delta sigma weight residual 112.00 100.62 11.38 1.40e+00 5.10e-01 6.60e+01 angle pdb=" CA PRO F 403 " pdb=" N PRO F 403 " pdb=" CD PRO F 403 " ideal model delta sigma weight residual 112.00 100.99 11.01 1.40e+00 5.10e-01 6.18e+01 angle pdb=" CA PRO E 198 " pdb=" N PRO E 198 " pdb=" CD PRO E 198 " ideal model delta sigma weight residual 112.00 101.71 10.29 1.40e+00 5.10e-01 5.40e+01 angle pdb=" C PRO C 255 " pdb=" CA PRO C 255 " pdb=" CB PRO C 255 " ideal model delta sigma weight residual 111.56 99.48 12.08 1.65e+00 3.67e-01 5.36e+01 ... (remaining 18583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 6471 16.00 - 32.00: 915 32.00 - 48.01: 271 48.01 - 64.01: 44 64.01 - 80.01: 9 Dihedral angle restraints: 7710 sinusoidal: 3042 harmonic: 4668 Sorted by residual: dihedral pdb=" C PRO C 255 " pdb=" N PRO C 255 " pdb=" CA PRO C 255 " pdb=" CB PRO C 255 " ideal model delta harmonic sigma weight residual -120.70 -104.81 -15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" CA LEU E 186 " pdb=" C LEU E 186 " pdb=" N PRO E 187 " pdb=" CA PRO E 187 " ideal model delta harmonic sigma weight residual -180.00 -162.78 -17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA PHE F 388 " pdb=" C PHE F 388 " pdb=" N GLU F 389 " pdb=" CA GLU F 389 " ideal model delta harmonic sigma weight residual -180.00 -162.96 -17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 7707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1808 0.063 - 0.126: 207 0.126 - 0.188: 21 0.188 - 0.251: 2 0.251 - 0.314: 2 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA PRO C 178 " pdb=" N PRO C 178 " pdb=" C PRO C 178 " pdb=" CB PRO C 178 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PRO F 403 " pdb=" N PRO F 403 " pdb=" C PRO F 403 " pdb=" CB PRO F 403 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA PRO C 255 " pdb=" N PRO C 255 " pdb=" C PRO C 255 " pdb=" CB PRO C 255 " both_signs ideal model delta sigma weight residual False 2.72 2.96 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2037 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 184 " -0.103 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO C 185 " 0.253 5.00e-02 4.00e+02 pdb=" CA PRO C 185 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 185 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 177 " 0.091 5.00e-02 4.00e+02 1.30e-01 2.69e+01 pdb=" N PRO C 178 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 186 " -0.066 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO E 187 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO E 187 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 187 " -0.053 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 144 2.66 - 3.22: 12404 3.22 - 3.78: 19390 3.78 - 4.34: 24764 4.34 - 4.90: 41735 Nonbonded interactions: 98437 Sorted by model distance: nonbonded pdb=" O ILE C 172 " pdb=" NH1 ARG C 176 " model vdw 2.097 3.120 nonbonded pdb=" O PHE E 201 " pdb=" OG1 THR E 204 " model vdw 2.174 3.040 nonbonded pdb=" N GLU D 399 " pdb=" OE1 GLU D 399 " model vdw 2.185 3.120 nonbonded pdb=" OH TYR B 372 " pdb=" O VAL B 392 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 372 " pdb=" O VAL A 392 " model vdw 2.218 3.040 ... (remaining 98432 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.740 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.004 0.158 13638 Z= 0.172 Angle : 0.764 15.126 18600 Z= 0.432 Chirality : 0.043 0.314 2040 Planarity : 0.007 0.147 2250 Dihedral : 15.899 80.011 4680 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 0.48 % Allowed : 21.30 % Favored : 78.22 % Cbeta Deviations : 0.07 % 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: -0.43 (0.22), residues: 1572 helix: 1.33 (0.17), residues: 906 sheet: None (None), residues: 0 loop : -2.76 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 243 TYR 0.022 0.001 TYR D 158 PHE 0.051 0.001 PHE D 277 TRP 0.039 0.001 TRP E 199 HIS 0.004 0.001 HIS E 364 Details of bonding type rmsd covalent geometry : bond 0.00438 (13632) covalent geometry : angle 0.76408 (18588) SS BOND : bond 0.00341 ( 6) SS BOND : angle 1.21873 ( 12) hydrogen bonds : bond 0.16634 ( 659) hydrogen bonds : angle 4.73305 ( 1977) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 278 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 176 ARG cc_start: 0.8165 (mmp80) cc_final: 0.7963 (mmp80) REVERT: C 393 ASN cc_start: 0.7776 (p0) cc_final: 0.7338 (p0) REVERT: D 151 LYS cc_start: 0.6544 (mttt) cc_final: 0.6214 (mmtt) REVERT: D 402 TRP cc_start: 0.8191 (t-100) cc_final: 0.7735 (t-100) REVERT: E 160 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7043 (t80) REVERT: E 209 MET cc_start: 0.7831 (mmp) cc_final: 0.7345 (mmp) REVERT: E 277 PHE cc_start: 0.6224 (m-80) cc_final: 0.6020 (m-80) REVERT: E 305 LEU cc_start: 0.8700 (mt) cc_final: 0.8475 (mt) REVERT: F 180 MET cc_start: 0.5902 (tmm) cc_final: 0.5627 (tmm) REVERT: F 183 TYR cc_start: 0.5460 (m-80) cc_final: 0.4893 (m-80) REVERT: F 192 ASP cc_start: 0.7151 (m-30) cc_final: 0.6800 (m-30) outliers start: 7 outliers final: 3 residues processed: 281 average time/residue: 0.1031 time to fit residues: 44.1075 Evaluate side-chains 245 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 241 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain F residue 165 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS C 291 HIS C 331 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.213612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158402 restraints weight = 17060.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148602 restraints weight = 19409.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144500 restraints weight = 13928.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144605 restraints weight = 13226.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144938 restraints weight = 11249.267| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13638 Z= 0.199 Angle : 0.654 10.355 18600 Z= 0.347 Chirality : 0.043 0.183 2040 Planarity : 0.005 0.075 2250 Dihedral : 5.062 50.835 1748 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 4.29 % Allowed : 19.23 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.35 (0.22), residues: 1572 helix: 1.53 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 379 TYR 0.017 0.002 TYR A 296 PHE 0.025 0.002 PHE B 298 TRP 0.016 0.001 TRP E 402 HIS 0.007 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00481 (13632) covalent geometry : angle 0.65407 (18588) SS BOND : bond 0.00310 ( 6) SS BOND : angle 0.86773 ( 12) hydrogen bonds : bond 0.06073 ( 659) hydrogen bonds : angle 3.61600 ( 1977) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7732 (mm-30) REVERT: C 172 ILE cc_start: 0.8859 (mm) cc_final: 0.8428 (mt) REVERT: D 160 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: D 209 MET cc_start: 0.8474 (mmm) cc_final: 0.8271 (mmm) REVERT: D 402 TRP cc_start: 0.8189 (t-100) cc_final: 0.7760 (t-100) REVERT: E 160 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7306 (t80) REVERT: E 191 LEU cc_start: 0.6106 (mm) cc_final: 0.5580 (mm) REVERT: E 209 MET cc_start: 0.8079 (mmp) cc_final: 0.7639 (mmp) REVERT: E 336 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7836 (t80) REVERT: F 183 TYR cc_start: 0.5838 (m-80) cc_final: 0.4884 (m-80) REVERT: F 192 ASP cc_start: 0.7393 (m-30) cc_final: 0.6946 (m-30) REVERT: F 398 ASN cc_start: 0.4509 (p0) cc_final: 0.3697 (p0) outliers start: 62 outliers final: 33 residues processed: 293 average time/residue: 0.1017 time to fit residues: 45.4830 Evaluate side-chains 268 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 PHE Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 392 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS C 331 ASN C 398 ASN ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.205054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128925 restraints weight = 17098.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130156 restraints weight = 11251.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131075 restraints weight = 8845.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131062 restraints weight = 8385.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131304 restraints weight = 8084.463| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 13638 Z= 0.309 Angle : 0.754 12.693 18600 Z= 0.399 Chirality : 0.046 0.198 2040 Planarity : 0.006 0.066 2250 Dihedral : 5.488 51.261 1744 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 6.43 % Allowed : 20.89 % Favored : 72.68 % 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: -0.75 (0.21), residues: 1572 helix: 1.11 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.80 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 379 TYR 0.022 0.003 TYR E 158 PHE 0.033 0.003 PHE B 298 TRP 0.018 0.002 TRP E 402 HIS 0.009 0.001 HIS E 342 Details of bonding type rmsd covalent geometry : bond 0.00750 (13632) covalent geometry : angle 0.75387 (18588) SS BOND : bond 0.00335 ( 6) SS BOND : angle 0.79737 ( 12) hydrogen bonds : bond 0.07434 ( 659) hydrogen bonds : angle 3.97514 ( 1977) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 264 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 180 MET cc_start: 0.8433 (tpp) cc_final: 0.8224 (tpp) REVERT: B 264 LYS cc_start: 0.5713 (tptt) cc_final: 0.5455 (mppt) REVERT: B 271 GLU cc_start: 0.7957 (tp30) cc_final: 0.7728 (tp30) REVERT: C 311 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6777 (t80) REVERT: C 318 ARG cc_start: 0.7412 (mmt180) cc_final: 0.6341 (mmt180) REVERT: C 370 ARG cc_start: 0.6273 (ptt-90) cc_final: 0.5697 (ptt90) REVERT: C 393 ASN cc_start: 0.8180 (p0) cc_final: 0.7980 (p0) REVERT: C 399 GLU cc_start: 0.4328 (pm20) cc_final: 0.3854 (pm20) REVERT: D 160 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: D 205 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7170 (mm-30) REVERT: D 207 CYS cc_start: 0.7830 (t) cc_final: 0.7483 (m) REVERT: D 209 MET cc_start: 0.8607 (mmm) cc_final: 0.8189 (mmm) REVERT: D 215 TRP cc_start: 0.8610 (t-100) cc_final: 0.7963 (t-100) REVERT: D 402 TRP cc_start: 0.8369 (t-100) cc_final: 0.7590 (t-100) REVERT: E 160 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7463 (t80) REVERT: E 209 MET cc_start: 0.8231 (mmp) cc_final: 0.7800 (mmp) REVERT: E 272 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7669 (mtmm) REVERT: E 297 MET cc_start: 0.6662 (tmm) cc_final: 0.6437 (tmm) REVERT: E 336 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7993 (t80) REVERT: E 370 ARG cc_start: 0.7972 (tmt170) cc_final: 0.7518 (tmt-80) REVERT: F 151 LYS cc_start: 0.6289 (mtpt) cc_final: 0.5539 (ptmt) REVERT: F 183 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.4895 (m-80) REVERT: F 280 TRP cc_start: 0.7093 (t-100) cc_final: 0.6495 (t60) REVERT: F 364 HIS cc_start: 0.6067 (OUTLIER) cc_final: 0.5283 (t70) REVERT: F 398 ASN cc_start: 0.5915 (p0) cc_final: 0.5272 (t0) outliers start: 93 outliers final: 58 residues processed: 327 average time/residue: 0.1041 time to fit residues: 51.4192 Evaluate side-chains 302 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 400 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN E 258 HIS ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.209605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133558 restraints weight = 17001.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138583 restraints weight = 10222.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139552 restraints weight = 7296.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140384 restraints weight = 6696.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140718 restraints weight = 7224.719| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13638 Z= 0.143 Angle : 0.600 12.357 18600 Z= 0.315 Chirality : 0.040 0.193 2040 Planarity : 0.004 0.056 2250 Dihedral : 5.002 51.377 1744 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 4.43 % Allowed : 23.03 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.22), residues: 1572 helix: 1.70 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.72 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 379 TYR 0.013 0.001 TYR A 158 PHE 0.024 0.001 PHE D 201 TRP 0.012 0.001 TRP D 215 HIS 0.005 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00334 (13632) covalent geometry : angle 0.59979 (18588) SS BOND : bond 0.00390 ( 6) SS BOND : angle 1.11109 ( 12) hydrogen bonds : bond 0.05079 ( 659) hydrogen bonds : angle 3.45701 ( 1977) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7827 (mm-30) REVERT: B 271 GLU cc_start: 0.7882 (tp30) cc_final: 0.7611 (tp30) REVERT: B 343 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7576 (mm-30) REVERT: C 370 ARG cc_start: 0.6247 (ptt-90) cc_final: 0.5516 (ptt90) REVERT: C 384 MET cc_start: 0.6736 (mmm) cc_final: 0.6466 (tpp) REVERT: C 393 ASN cc_start: 0.7974 (p0) cc_final: 0.7699 (p0) REVERT: D 205 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6927 (mm-30) REVERT: D 209 MET cc_start: 0.8567 (mmm) cc_final: 0.8176 (mmm) REVERT: D 215 TRP cc_start: 0.8614 (t-100) cc_final: 0.7958 (t-100) REVERT: D 347 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8519 (tp) REVERT: D 402 TRP cc_start: 0.8290 (t-100) cc_final: 0.7620 (t-100) REVERT: E 160 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7497 (t80) REVERT: E 209 MET cc_start: 0.8468 (mmp) cc_final: 0.8015 (mmp) REVERT: E 336 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7930 (t80) REVERT: E 370 ARG cc_start: 0.7823 (tmt170) cc_final: 0.7613 (tmt-80) REVERT: F 151 LYS cc_start: 0.6429 (mtpt) cc_final: 0.5574 (ptmt) REVERT: F 161 ILE cc_start: 0.8143 (mm) cc_final: 0.7940 (tp) REVERT: F 183 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.4930 (m-80) REVERT: F 280 TRP cc_start: 0.7155 (t-100) cc_final: 0.6798 (t60) REVERT: F 398 ASN cc_start: 0.5826 (p0) cc_final: 0.5251 (t0) outliers start: 64 outliers final: 44 residues processed: 308 average time/residue: 0.1041 time to fit residues: 48.5964 Evaluate side-chains 293 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 107 optimal weight: 0.0670 chunk 135 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 53 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 HIS E 291 HIS F 174 HIS ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.211791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142753 restraints weight = 17001.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142534 restraints weight = 10855.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142086 restraints weight = 8628.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142336 restraints weight = 8891.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142469 restraints weight = 8031.996| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13638 Z= 0.119 Angle : 0.575 12.975 18600 Z= 0.300 Chirality : 0.039 0.186 2040 Planarity : 0.004 0.048 2250 Dihedral : 4.546 51.466 1742 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 4.43 % Allowed : 24.41 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.22), residues: 1572 helix: 2.03 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 379 TYR 0.019 0.001 TYR E 158 PHE 0.026 0.001 PHE D 201 TRP 0.012 0.001 TRP E 402 HIS 0.005 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00267 (13632) covalent geometry : angle 0.57371 (18588) SS BOND : bond 0.00537 ( 6) SS BOND : angle 1.34267 ( 12) hydrogen bonds : bond 0.04287 ( 659) hydrogen bonds : angle 3.27608 ( 1977) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 297 MET cc_start: 0.8302 (tpt) cc_final: 0.8011 (mmm) REVERT: B 271 GLU cc_start: 0.7797 (tp30) cc_final: 0.7521 (tp30) REVERT: C 318 ARG cc_start: 0.7493 (mmt180) cc_final: 0.6836 (mmt180) REVERT: C 384 MET cc_start: 0.6952 (mmm) cc_final: 0.6322 (mtt) REVERT: C 393 ASN cc_start: 0.7675 (p0) cc_final: 0.7456 (p0) REVERT: D 180 MET cc_start: 0.5540 (ptm) cc_final: 0.5339 (ppp) REVERT: D 205 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6688 (mm-30) REVERT: D 209 MET cc_start: 0.8579 (mmm) cc_final: 0.8193 (mmm) REVERT: D 215 TRP cc_start: 0.8580 (t-100) cc_final: 0.7820 (t-100) REVERT: D 402 TRP cc_start: 0.8190 (t-100) cc_final: 0.7525 (t-100) REVERT: E 160 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: E 209 MET cc_start: 0.8357 (mmp) cc_final: 0.7987 (mmm) REVERT: E 247 MET cc_start: 0.7470 (mmp) cc_final: 0.7221 (mmt) REVERT: E 272 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7730 (mtmm) REVERT: E 336 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7958 (t80) REVERT: E 370 ARG cc_start: 0.7848 (tmt170) cc_final: 0.7594 (tmt-80) REVERT: E 384 MET cc_start: 0.6135 (mmt) cc_final: 0.5841 (mmp) REVERT: F 151 LYS cc_start: 0.6523 (mtpt) cc_final: 0.5662 (ptmt) REVERT: F 180 MET cc_start: 0.6215 (tmm) cc_final: 0.5984 (tpt) REVERT: F 183 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.4836 (m-80) REVERT: F 280 TRP cc_start: 0.7267 (t-100) cc_final: 0.7006 (t60) REVERT: F 398 ASN cc_start: 0.5638 (p0) cc_final: 0.5169 (t0) outliers start: 64 outliers final: 48 residues processed: 308 average time/residue: 0.1000 time to fit residues: 47.0643 Evaluate side-chains 289 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 118 optimal weight: 0.1980 chunk 55 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 144 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 116 optimal weight: 0.0570 overall best weight: 1.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 HIS E 331 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.207170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131468 restraints weight = 16999.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135197 restraints weight = 10121.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136481 restraints weight = 7298.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137074 restraints weight = 8085.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137030 restraints weight = 6986.861| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13638 Z= 0.183 Angle : 0.628 14.437 18600 Z= 0.328 Chirality : 0.041 0.189 2040 Planarity : 0.004 0.045 2250 Dihedral : 4.666 50.974 1742 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 5.46 % Allowed : 24.07 % Favored : 70.47 % 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: -0.06 (0.22), residues: 1572 helix: 1.78 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.67 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 243 TYR 0.016 0.002 TYR A 158 PHE 0.020 0.001 PHE A 298 TRP 0.011 0.001 TRP B 320 HIS 0.007 0.001 HIS E 291 Details of bonding type rmsd covalent geometry : bond 0.00439 (13632) covalent geometry : angle 0.62698 (18588) SS BOND : bond 0.00452 ( 6) SS BOND : angle 1.32421 ( 12) hydrogen bonds : bond 0.05414 ( 659) hydrogen bonds : angle 3.41455 ( 1977) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 258 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 180 MET cc_start: 0.8120 (tpp) cc_final: 0.7888 (tpp) REVERT: B 271 GLU cc_start: 0.7846 (tp30) cc_final: 0.7556 (tp30) REVERT: C 318 ARG cc_start: 0.7395 (mmt180) cc_final: 0.6664 (mmt180) REVERT: D 205 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6646 (mm-30) REVERT: D 209 MET cc_start: 0.8582 (mmm) cc_final: 0.8167 (mmm) REVERT: D 215 TRP cc_start: 0.8572 (t-100) cc_final: 0.8079 (t-100) REVERT: D 347 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8545 (tp) REVERT: D 402 TRP cc_start: 0.8222 (t-100) cc_final: 0.7575 (t-100) REVERT: E 160 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: E 209 MET cc_start: 0.8419 (mmp) cc_final: 0.8071 (mmm) REVERT: E 272 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7675 (mtmm) REVERT: E 336 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7982 (t80) REVERT: F 151 LYS cc_start: 0.6556 (mtpt) cc_final: 0.5597 (pttp) REVERT: F 169 ILE cc_start: 0.8099 (mm) cc_final: 0.7822 (tp) REVERT: F 180 MET cc_start: 0.6352 (tmm) cc_final: 0.6045 (tmm) REVERT: F 183 TYR cc_start: 0.5922 (OUTLIER) cc_final: 0.4685 (m-80) REVERT: F 209 MET cc_start: 0.7280 (tpt) cc_final: 0.6677 (tpp) REVERT: F 280 TRP cc_start: 0.7230 (t-100) cc_final: 0.6887 (t60) REVERT: F 398 ASN cc_start: 0.5826 (p0) cc_final: 0.5429 (t0) outliers start: 79 outliers final: 62 residues processed: 313 average time/residue: 0.0764 time to fit residues: 37.3214 Evaluate side-chains 310 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 244 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 331 ASN Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 131 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN C 398 ASN D 364 HIS ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.209485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137629 restraints weight = 17011.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138291 restraints weight = 10711.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138526 restraints weight = 8380.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138814 restraints weight = 7589.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139153 restraints weight = 7412.071| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13638 Z= 0.132 Angle : 0.599 13.783 18600 Z= 0.312 Chirality : 0.040 0.190 2040 Planarity : 0.004 0.043 2250 Dihedral : 4.508 50.627 1742 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 4.84 % Allowed : 25.45 % Favored : 69.71 % 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: 0.12 (0.22), residues: 1572 helix: 1.93 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.60 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 243 TYR 0.019 0.001 TYR E 158 PHE 0.012 0.001 PHE C 385 TRP 0.013 0.001 TRP E 402 HIS 0.007 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00306 (13632) covalent geometry : angle 0.59865 (18588) SS BOND : bond 0.00646 ( 6) SS BOND : angle 1.22207 ( 12) hydrogen bonds : bond 0.04591 ( 659) hydrogen bonds : angle 3.30352 ( 1977) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 253 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 297 MET cc_start: 0.8339 (tpt) cc_final: 0.8013 (mmm) REVERT: A 347 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7380 (pt) REVERT: B 271 GLU cc_start: 0.7780 (tp30) cc_final: 0.7462 (tp30) REVERT: C 318 ARG cc_start: 0.7445 (mmt180) cc_final: 0.6669 (mmt180) REVERT: C 384 MET cc_start: 0.6864 (mmm) cc_final: 0.6262 (mtt) REVERT: D 205 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6625 (mm-30) REVERT: D 209 MET cc_start: 0.8667 (mmm) cc_final: 0.8218 (mmm) REVERT: D 215 TRP cc_start: 0.8532 (t-100) cc_final: 0.8077 (t-100) REVERT: D 382 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: D 402 TRP cc_start: 0.8178 (t-100) cc_final: 0.7502 (t-100) REVERT: E 160 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: E 209 MET cc_start: 0.8468 (mmp) cc_final: 0.8108 (mmm) REVERT: E 272 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7694 (mtmm) REVERT: E 336 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8023 (t80) REVERT: F 151 LYS cc_start: 0.6484 (mtpt) cc_final: 0.5551 (pttp) REVERT: F 169 ILE cc_start: 0.7906 (mm) cc_final: 0.7623 (tp) REVERT: F 180 MET cc_start: 0.6513 (tmm) cc_final: 0.6215 (tmm) REVERT: F 183 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.4810 (m-80) REVERT: F 209 MET cc_start: 0.7251 (tpt) cc_final: 0.6631 (tpp) REVERT: F 280 TRP cc_start: 0.7326 (t-100) cc_final: 0.7016 (t60) REVERT: F 398 ASN cc_start: 0.5948 (p0) cc_final: 0.5542 (t0) outliers start: 70 outliers final: 57 residues processed: 301 average time/residue: 0.0794 time to fit residues: 36.9165 Evaluate side-chains 302 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 240 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 331 ASN Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN C 364 HIS E 364 HIS ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.209921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142228 restraints weight = 16949.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140080 restraints weight = 11053.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140239 restraints weight = 8859.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140999 restraints weight = 8625.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141029 restraints weight = 8421.483| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13638 Z= 0.130 Angle : 0.591 15.373 18600 Z= 0.309 Chirality : 0.040 0.196 2040 Planarity : 0.004 0.042 2250 Dihedral : 4.444 50.269 1742 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.98 % Allowed : 25.24 % Favored : 69.78 % 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 aren not related in a simple way. whole: 0.21 (0.22), residues: 1572 helix: 2.00 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.55 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 243 TYR 0.013 0.001 TYR A 158 PHE 0.021 0.001 PHE B 387 TRP 0.021 0.001 TRP E 402 HIS 0.005 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00300 (13632) covalent geometry : angle 0.59011 (18588) SS BOND : bond 0.00395 ( 6) SS BOND : angle 1.08266 ( 12) hydrogen bonds : bond 0.04444 ( 659) hydrogen bonds : angle 3.26755 ( 1977) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 254 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 347 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7262 (pt) REVERT: C 384 MET cc_start: 0.6780 (mmm) cc_final: 0.6348 (mtt) REVERT: D 205 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6833 (mm-30) REVERT: D 209 MET cc_start: 0.8595 (mmm) cc_final: 0.8156 (mmm) REVERT: D 215 TRP cc_start: 0.8558 (t-100) cc_final: 0.8148 (t-100) REVERT: D 343 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: D 399 GLU cc_start: 0.5722 (pm20) cc_final: 0.5400 (pm20) REVERT: D 402 TRP cc_start: 0.8121 (t-100) cc_final: 0.7547 (t-100) REVERT: E 205 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6990 (mm-30) REVERT: E 209 MET cc_start: 0.8401 (mmp) cc_final: 0.8081 (mmm) REVERT: E 272 LYS cc_start: 0.7851 (mtpp) cc_final: 0.7576 (mtmm) REVERT: E 336 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7988 (t80) REVERT: F 151 LYS cc_start: 0.6591 (mtpt) cc_final: 0.5617 (pttt) REVERT: F 180 MET cc_start: 0.6162 (tmm) cc_final: 0.5938 (tmm) REVERT: F 183 TYR cc_start: 0.5830 (OUTLIER) cc_final: 0.4593 (m-80) REVERT: F 209 MET cc_start: 0.7246 (tpt) cc_final: 0.6628 (tpp) REVERT: F 398 ASN cc_start: 0.5754 (p0) cc_final: 0.5520 (t0) outliers start: 72 outliers final: 60 residues processed: 308 average time/residue: 0.0812 time to fit residues: 38.6136 Evaluate side-chains 306 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 242 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 141 optimal weight: 0.0870 chunk 139 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.210724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142405 restraints weight = 16968.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141034 restraints weight = 10348.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140556 restraints weight = 8856.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141823 restraints weight = 8714.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141765 restraints weight = 8102.083| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13638 Z= 0.127 Angle : 0.616 15.494 18600 Z= 0.322 Chirality : 0.040 0.187 2040 Planarity : 0.004 0.041 2250 Dihedral : 4.202 19.345 1740 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 5.05 % Allowed : 25.86 % Favored : 69.09 % 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: 0.29 (0.22), residues: 1572 helix: 2.06 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.51 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 243 TYR 0.020 0.001 TYR E 158 PHE 0.018 0.001 PHE B 387 TRP 0.021 0.001 TRP E 402 HIS 0.005 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00292 (13632) covalent geometry : angle 0.61598 (18588) SS BOND : bond 0.00383 ( 6) SS BOND : angle 0.99881 ( 12) hydrogen bonds : bond 0.04301 ( 659) hydrogen bonds : angle 3.23576 ( 1977) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 252 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7745 (mm-30) REVERT: A 347 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7290 (pt) REVERT: C 384 MET cc_start: 0.6866 (mmm) cc_final: 0.6442 (mtt) REVERT: D 205 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6771 (mm-30) REVERT: D 209 MET cc_start: 0.8606 (mmm) cc_final: 0.8156 (mmm) REVERT: D 215 TRP cc_start: 0.8547 (t-100) cc_final: 0.8149 (t-100) REVERT: D 343 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: D 399 GLU cc_start: 0.5895 (pm20) cc_final: 0.5546 (pm20) REVERT: D 402 TRP cc_start: 0.8115 (t-100) cc_final: 0.7545 (t-100) REVERT: E 205 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6759 (mm-30) REVERT: E 209 MET cc_start: 0.8487 (mmp) cc_final: 0.8126 (mmm) REVERT: E 336 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8054 (t80) REVERT: F 151 LYS cc_start: 0.6513 (mtpt) cc_final: 0.5579 (pttp) REVERT: F 180 MET cc_start: 0.6382 (tmm) cc_final: 0.5992 (tpt) REVERT: F 183 TYR cc_start: 0.5867 (OUTLIER) cc_final: 0.4602 (m-80) REVERT: F 398 ASN cc_start: 0.5814 (p0) cc_final: 0.5587 (t0) outliers start: 73 outliers final: 64 residues processed: 309 average time/residue: 0.0835 time to fit residues: 40.1213 Evaluate side-chains 304 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 236 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 0.0870 chunk 125 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.210425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140935 restraints weight = 16823.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140627 restraints weight = 10215.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140473 restraints weight = 8577.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141523 restraints weight = 8156.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141558 restraints weight = 7457.590| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13638 Z= 0.132 Angle : 0.619 14.657 18600 Z= 0.324 Chirality : 0.040 0.207 2040 Planarity : 0.004 0.041 2250 Dihedral : 4.176 19.554 1740 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 5.05 % Allowed : 26.14 % Favored : 68.81 % 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: 0.24 (0.22), residues: 1572 helix: 2.00 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.50 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 243 TYR 0.012 0.001 TYR A 158 PHE 0.017 0.001 PHE B 387 TRP 0.022 0.001 TRP E 402 HIS 0.005 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00305 (13632) covalent geometry : angle 0.61896 (18588) SS BOND : bond 0.00365 ( 6) SS BOND : angle 0.92466 ( 12) hydrogen bonds : bond 0.04324 ( 659) hydrogen bonds : angle 3.27936 ( 1977) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 248 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 181 GLN cc_start: 0.8240 (pp30) cc_final: 0.7891 (pp30) REVERT: A 347 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7245 (pt) REVERT: C 384 MET cc_start: 0.6706 (mmm) cc_final: 0.6268 (mtt) REVERT: D 180 MET cc_start: 0.5598 (ppp) cc_final: 0.5220 (mmt) REVERT: D 209 MET cc_start: 0.8655 (mmm) cc_final: 0.8250 (mmm) REVERT: D 215 TRP cc_start: 0.8544 (t-100) cc_final: 0.8145 (t-100) REVERT: D 333 PHE cc_start: 0.8253 (m-80) cc_final: 0.7927 (m-80) REVERT: D 343 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: D 399 GLU cc_start: 0.5802 (pm20) cc_final: 0.5399 (pm20) REVERT: D 402 TRP cc_start: 0.8131 (t-100) cc_final: 0.7553 (t-100) REVERT: E 203 MET cc_start: 0.8031 (mtt) cc_final: 0.7804 (tpt) REVERT: E 205 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7084 (mm-30) REVERT: E 209 MET cc_start: 0.8567 (mmp) cc_final: 0.8224 (mmm) REVERT: E 336 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.8088 (t80) REVERT: E 384 MET cc_start: 0.6074 (mmt) cc_final: 0.5809 (mmp) REVERT: F 151 LYS cc_start: 0.6397 (mtpt) cc_final: 0.5537 (pttp) REVERT: F 180 MET cc_start: 0.6672 (tmm) cc_final: 0.6273 (tpt) REVERT: F 183 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.4619 (m-80) REVERT: F 398 ASN cc_start: 0.5869 (p0) cc_final: 0.5616 (t0) outliers start: 73 outliers final: 66 residues processed: 304 average time/residue: 0.0853 time to fit residues: 40.1094 Evaluate side-chains 314 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 244 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 0.0070 chunk 88 optimal weight: 0.0020 chunk 135 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.211582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140745 restraints weight = 16764.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140665 restraints weight = 10390.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143005 restraints weight = 8808.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142880 restraints weight = 7338.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143359 restraints weight = 7430.428| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13638 Z= 0.124 Angle : 0.611 15.249 18600 Z= 0.320 Chirality : 0.040 0.200 2040 Planarity : 0.004 0.040 2250 Dihedral : 4.179 25.033 1740 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 4.43 % Allowed : 26.76 % Favored : 68.81 % 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: 0.33 (0.22), residues: 1572 helix: 2.10 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.50 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 243 TYR 0.022 0.001 TYR E 158 PHE 0.022 0.001 PHE D 201 TRP 0.021 0.001 TRP E 402 HIS 0.006 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00283 (13632) covalent geometry : angle 0.61099 (18588) SS BOND : bond 0.00401 ( 6) SS BOND : angle 1.13045 ( 12) hydrogen bonds : bond 0.04056 ( 659) hydrogen bonds : angle 3.23677 ( 1977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2562.43 seconds wall clock time: 44 minutes 53.37 seconds (2693.37 seconds total)