Starting phenix.real_space_refine on Thu May 15 11:41:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9y_37385/05_2025/8w9y_37385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9y_37385/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9y_37385/05_2025/8w9y_37385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9y_37385/05_2025/8w9y_37385.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9y_37385/05_2025/8w9y_37385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9y_37385/05_2025/8w9y_37385.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.85, per 1000 atoms: 0.60 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: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.94 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: 2.83 Time building geometry restraints manager: 3.53 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: 0.02 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: 1.370 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.140 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.340 ------------------------------------------------------------------------------- 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 : 9.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (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 TRP 0.039 0.001 TRP E 199 HIS 0.004 0.001 HIS E 364 PHE 0.051 0.001 PHE D 277 TYR 0.022 0.001 TYR D 158 ARG 0.002 0.000 ARG C 243 Details of bonding type rmsd hydrogen bonds : bond 0.16634 ( 659) hydrogen bonds : angle 4.73305 ( 1977) SS BOND : bond 0.00341 ( 6) SS BOND : angle 1.21873 ( 12) covalent geometry : bond 0.00438 (13632) covalent geometry : angle 0.76408 (18588) *********************** 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 : 1.343 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: 0.2164 time to fit residues: 90.8313 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 : 1.353 ------------------------------------------------------------------------------- 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 131 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4426 r_free = 0.4426 target = 0.212356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156698 restraints weight = 17007.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144039 restraints weight = 19743.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140353 restraints weight = 14707.752| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13638 Z= 0.219 Angle : 0.677 10.411 18600 Z= 0.359 Chirality : 0.043 0.185 2040 Planarity : 0.005 0.073 2250 Dihedral : 5.144 50.627 1748 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 4.36 % Allowed : 19.23 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1572 helix: 1.44 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.77 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 402 HIS 0.005 0.001 HIS E 342 PHE 0.029 0.002 PHE B 298 TYR 0.018 0.002 TYR F 149 ARG 0.004 0.000 ARG F 275 Details of bonding type rmsd hydrogen bonds : bond 0.06433 ( 659) hydrogen bonds : angle 3.69654 ( 1977) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.92076 ( 12) covalent geometry : bond 0.00532 (13632) covalent geometry : angle 0.67691 (18588) *********************** 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 317 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.6081 (tttp) cc_final: 0.5880 (tttp) REVERT: C 172 ILE cc_start: 0.8868 (mm) cc_final: 0.8434 (mt) REVERT: D 160 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: D 402 TRP cc_start: 0.8200 (t-100) cc_final: 0.7718 (t-100) REVERT: E 160 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7300 (t80) REVERT: E 209 MET cc_start: 0.8042 (mmp) cc_final: 0.7572 (mmp) REVERT: E 248 PHE cc_start: 0.8587 (t80) cc_final: 0.8386 (t80) REVERT: E 336 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7830 (t80) REVERT: F 192 ASP cc_start: 0.7377 (m-30) cc_final: 0.7171 (m-30) REVERT: F 314 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: F 315 TYR cc_start: 0.7042 (m-80) cc_final: 0.6550 (m-80) REVERT: F 398 ASN cc_start: 0.4671 (p0) cc_final: 0.3834 (p0) outliers start: 63 outliers final: 36 residues processed: 294 average time/residue: 0.2179 time to fit residues: 97.1236 Evaluate side-chains 271 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 391 ASN 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 305 LEU 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 359 LEU Chi-restraints excluded: chain E residue 365 THR 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 312 VAL Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 400 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 92 optimal weight: 0.0970 chunk 128 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ** C 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 398 ASN D 364 HIS ** 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 = 0.4458 r_free = 0.4458 target = 0.216153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.161416 restraints weight = 17079.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150304 restraints weight = 18424.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147576 restraints weight = 14346.628| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13638 Z= 0.123 Angle : 0.577 12.402 18600 Z= 0.301 Chirality : 0.039 0.198 2040 Planarity : 0.004 0.062 2250 Dihedral : 4.712 50.840 1744 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.67 % Allowed : 21.02 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1572 helix: 1.94 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.66 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 402 HIS 0.005 0.001 HIS C 291 PHE 0.041 0.001 PHE E 277 TYR 0.018 0.001 TYR E 158 ARG 0.005 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 659) hydrogen bonds : angle 3.34976 ( 1977) SS BOND : bond 0.00280 ( 6) SS BOND : angle 0.66192 ( 12) covalent geometry : bond 0.00279 (13632) covalent geometry : angle 0.57726 (18588) *********************** 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 312 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.5433 (tptt) cc_final: 0.5045 (mppt) REVERT: B 271 GLU cc_start: 0.7815 (tp30) cc_final: 0.7585 (tp30) REVERT: B 343 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7732 (mm-30) REVERT: C 172 ILE cc_start: 0.8742 (mm) cc_final: 0.8463 (mt) REVERT: C 176 ARG cc_start: 0.8527 (mmp80) cc_final: 0.8119 (mmp80) REVERT: C 393 ASN cc_start: 0.7798 (p0) cc_final: 0.7549 (p0) REVERT: D 203 MET cc_start: 0.8412 (tpt) cc_final: 0.8168 (mmm) REVERT: D 209 MET cc_start: 0.8338 (mmm) cc_final: 0.7860 (mmm) REVERT: D 370 ARG cc_start: 0.7370 (ptm-80) cc_final: 0.7136 (ptm-80) REVERT: D 402 TRP cc_start: 0.8272 (t-100) cc_final: 0.7721 (t-100) REVERT: E 160 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7241 (t80) REVERT: E 191 LEU cc_start: 0.6354 (mm) cc_final: 0.5804 (mm) REVERT: E 209 MET cc_start: 0.8313 (mmp) cc_final: 0.7900 (mmp) REVERT: E 336 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7814 (t80) REVERT: F 183 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5080 (m-80) REVERT: F 285 MET cc_start: 0.7094 (mpp) cc_final: 0.6853 (mpp) REVERT: F 398 ASN cc_start: 0.4856 (p0) cc_final: 0.4242 (p0) outliers start: 53 outliers final: 27 residues processed: 291 average time/residue: 0.2039 time to fit residues: 89.5624 Evaluate side-chains 270 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 167 SER 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 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 390 CYS 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 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 222 HIS C 398 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.212296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137925 restraints weight = 16868.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141161 restraints weight = 10200.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141556 restraints weight = 7560.301| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13638 Z= 0.145 Angle : 0.594 12.130 18600 Z= 0.310 Chirality : 0.040 0.188 2040 Planarity : 0.004 0.055 2250 Dihedral : 4.539 50.721 1742 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.29 % Allowed : 21.09 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1572 helix: 1.95 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.64 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 402 HIS 0.004 0.001 HIS E 342 PHE 0.025 0.001 PHE D 201 TYR 0.018 0.001 TYR E 158 ARG 0.003 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 659) hydrogen bonds : angle 3.34047 ( 1977) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.66481 ( 12) covalent geometry : bond 0.00341 (13632) covalent geometry : angle 0.59364 (18588) *********************** 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 324 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 271 GLU cc_start: 0.7923 (tp30) cc_final: 0.7655 (tp30) REVERT: B 343 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7739 (mm-30) REVERT: C 172 ILE cc_start: 0.8738 (mm) cc_final: 0.8442 (mt) REVERT: C 176 ARG cc_start: 0.8384 (mmp80) cc_final: 0.7722 (mmp80) REVERT: C 370 ARG cc_start: 0.6115 (ptt-90) cc_final: 0.5533 (ptt90) REVERT: C 384 MET cc_start: 0.6717 (mmm) cc_final: 0.6446 (tpp) REVERT: C 393 ASN cc_start: 0.7996 (p0) cc_final: 0.7724 (p0) REVERT: D 203 MET cc_start: 0.8624 (tpt) cc_final: 0.8196 (mmm) REVERT: D 209 MET cc_start: 0.8583 (mmm) cc_final: 0.8032 (mmm) REVERT: D 215 TRP cc_start: 0.8538 (t-100) cc_final: 0.7143 (t-100) REVERT: D 370 ARG cc_start: 0.7397 (ptm-80) cc_final: 0.7138 (ptm-80) REVERT: D 402 TRP cc_start: 0.8343 (t-100) cc_final: 0.7650 (t-100) REVERT: E 160 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: E 209 MET cc_start: 0.8505 (mmp) cc_final: 0.8017 (mmp) REVERT: E 336 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7941 (t80) REVERT: E 370 ARG cc_start: 0.7980 (tmt-80) cc_final: 0.7502 (tmt-80) REVERT: F 151 LYS cc_start: 0.5871 (mtpt) cc_final: 0.5359 (ptmt) REVERT: F 183 TYR cc_start: 0.6244 (OUTLIER) cc_final: 0.4993 (m-80) REVERT: F 275 ARG cc_start: 0.5593 (tpt170) cc_final: 0.5391 (tpt170) outliers start: 62 outliers final: 46 residues processed: 305 average time/residue: 0.2197 time to fit residues: 100.7893 Evaluate side-chains 293 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 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 347 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 160 PHE 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 261 CYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 293 CYS 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 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 364 HIS 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 316 THR Chi-restraints excluded: chain E residue 160 PHE 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 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 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 384 MET Chi-restraints excluded: chain F residue 392 VAL 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 62 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 24 optimal weight: 0.0170 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.208111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136420 restraints weight = 17080.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135546 restraints weight = 10327.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136060 restraints weight = 8192.657| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13638 Z= 0.196 Angle : 0.644 13.884 18600 Z= 0.338 Chirality : 0.041 0.198 2040 Planarity : 0.004 0.049 2250 Dihedral : 4.729 50.637 1742 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 5.33 % Allowed : 21.72 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.22), residues: 1572 helix: 1.64 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.64 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 402 HIS 0.005 0.001 HIS E 342 PHE 0.022 0.002 PHE B 298 TYR 0.020 0.002 TYR E 158 ARG 0.003 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.05819 ( 659) hydrogen bonds : angle 3.51974 ( 1977) SS BOND : bond 0.00398 ( 6) SS BOND : angle 0.67770 ( 12) covalent geometry : bond 0.00469 (13632) covalent geometry : angle 0.64384 (18588) *********************** 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 337 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 260 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 180 MET cc_start: 0.7433 (mtt) cc_final: 0.7190 (mtt) REVERT: B 271 GLU cc_start: 0.7934 (tp30) cc_final: 0.7643 (tp30) REVERT: C 384 MET cc_start: 0.6946 (mmm) cc_final: 0.6322 (mtt) REVERT: C 393 ASN cc_start: 0.7937 (p0) cc_final: 0.7635 (p0) REVERT: D 209 MET cc_start: 0.8606 (mmm) cc_final: 0.8143 (mmm) REVERT: D 215 TRP cc_start: 0.8640 (t-100) cc_final: 0.8019 (t-100) REVERT: D 370 ARG cc_start: 0.7376 (ptm-80) cc_final: 0.7110 (ptm-80) REVERT: D 402 TRP cc_start: 0.8194 (t-100) cc_final: 0.7499 (t-100) REVERT: E 160 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: E 209 MET cc_start: 0.8409 (mmp) cc_final: 0.7976 (mmp) REVERT: E 336 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7900 (t80) REVERT: E 370 ARG cc_start: 0.7997 (tmt-80) cc_final: 0.7455 (tmt-80) REVERT: E 402 TRP cc_start: 0.6680 (t-100) cc_final: 0.6418 (t-100) REVERT: F 151 LYS cc_start: 0.6300 (mtpt) cc_final: 0.5503 (ptmt) REVERT: F 165 PHE cc_start: 0.7434 (t80) cc_final: 0.7233 (t80) REVERT: F 183 TYR cc_start: 0.6135 (OUTLIER) cc_final: 0.4689 (m-80) outliers start: 77 outliers final: 58 residues processed: 311 average time/residue: 0.2093 time to fit residues: 98.5340 Evaluate side-chains 298 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 238 THR Chi-restraints excluded: chain A residue 264 LYS 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 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL 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 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 390 CYS Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 241 LEU 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 312 VAL Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 364 HIS 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 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 216 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain E residue 285 MET 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 246 THR 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 396 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 5 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 139 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.211673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141605 restraints weight = 17056.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142358 restraints weight = 11848.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141538 restraints weight = 10382.452| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3443 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 : 0.579 13.356 18600 Z= 0.301 Chirality : 0.039 0.180 2040 Planarity : 0.004 0.044 2250 Dihedral : 4.420 50.182 1742 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 4.22 % Allowed : 23.65 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1572 helix: 2.09 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 402 HIS 0.006 0.001 HIS C 291 PHE 0.016 0.001 PHE F 165 TYR 0.015 0.001 TYR D 158 ARG 0.004 0.000 ARG F 243 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 659) hydrogen bonds : angle 3.24663 ( 1977) SS BOND : bond 0.00312 ( 6) SS BOND : angle 0.65406 ( 12) covalent geometry : bond 0.00266 (13632) covalent geometry : angle 0.57885 (18588) *********************** 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 317 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 256 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7755 (mm-30) REVERT: A 297 MET cc_start: 0.8323 (tpt) cc_final: 0.7982 (mmm) REVERT: B 209 MET cc_start: 0.7094 (mtt) cc_final: 0.6759 (mtt) REVERT: B 264 LYS cc_start: 0.5960 (tttp) cc_final: 0.5454 (mppt) REVERT: B 271 GLU cc_start: 0.7797 (tp30) cc_final: 0.7490 (tp30) REVERT: B 343 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7667 (mm-30) REVERT: C 393 ASN cc_start: 0.7901 (p0) cc_final: 0.7591 (p0) REVERT: D 209 MET cc_start: 0.8575 (mmm) cc_final: 0.8093 (mmm) REVERT: D 215 TRP cc_start: 0.8603 (t-100) cc_final: 0.7832 (t-100) REVERT: D 402 TRP cc_start: 0.8202 (t-100) cc_final: 0.7565 (t-100) REVERT: E 209 MET cc_start: 0.8431 (mmp) cc_final: 0.8002 (mmp) REVERT: E 272 LYS cc_start: 0.7967 (mtpp) cc_final: 0.7730 (mtmm) REVERT: E 336 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7881 (t80) REVERT: E 370 ARG cc_start: 0.8020 (tmt-80) cc_final: 0.7389 (tmt-80) REVERT: E 402 TRP cc_start: 0.6624 (t-100) cc_final: 0.6213 (t-100) REVERT: F 151 LYS cc_start: 0.6277 (mtpt) cc_final: 0.5481 (ptmt) REVERT: F 183 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.4814 (m-80) outliers start: 61 outliers final: 47 residues processed: 298 average time/residue: 0.1984 time to fit residues: 90.6815 Evaluate side-chains 292 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 264 LYS 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 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL 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 288 THR Chi-restraints excluded: chain B residue 293 CYS 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 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 331 ASN Chi-restraints excluded: chain C residue 338 ILE 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 316 THR Chi-restraints excluded: chain D residue 364 HIS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 318 ARG Chi-restraints excluded: chain E residue 336 PHE Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 246 THR 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 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 90 optimal weight: 7.9990 chunk 93 optimal weight: 0.0770 chunk 153 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 0.0020 chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.4946 ------------------------------------------------------------------------------- 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 ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 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 = 0.4431 r_free = 0.4431 target = 0.212674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141062 restraints weight = 16906.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142796 restraints weight = 10682.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143701 restraints weight = 8095.873| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13638 Z= 0.114 Angle : 0.573 15.213 18600 Z= 0.298 Chirality : 0.039 0.184 2040 Planarity : 0.004 0.042 2250 Dihedral : 4.164 19.191 1740 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 4.01 % Allowed : 24.76 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1572 helix: 2.18 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.50 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 402 HIS 0.006 0.001 HIS C 291 PHE 0.023 0.001 PHE F 165 TYR 0.018 0.001 TYR E 158 ARG 0.002 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 659) hydrogen bonds : angle 3.18714 ( 1977) SS BOND : bond 0.00557 ( 6) SS BOND : angle 0.96273 ( 12) covalent geometry : bond 0.00257 (13632) covalent geometry : angle 0.57315 (18588) *********************** 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 312 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 254 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 347 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7310 (pt) REVERT: B 209 MET cc_start: 0.6998 (mtt) cc_final: 0.6679 (mtt) REVERT: B 264 LYS cc_start: 0.5872 (tttp) cc_final: 0.5406 (mppt) REVERT: C 384 MET cc_start: 0.6528 (mmm) cc_final: 0.6017 (mtt) REVERT: C 393 ASN cc_start: 0.7680 (p0) cc_final: 0.7429 (p0) REVERT: D 209 MET cc_start: 0.8611 (mmm) cc_final: 0.8186 (mmm) REVERT: D 215 TRP cc_start: 0.8524 (t-100) cc_final: 0.8021 (t-100) REVERT: D 370 ARG cc_start: 0.7292 (ptm-80) cc_final: 0.7047 (ptm-80) REVERT: D 402 TRP cc_start: 0.8160 (t-100) cc_final: 0.7531 (t-100) REVERT: E 205 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7110 (mm-30) REVERT: E 209 MET cc_start: 0.8460 (mmp) cc_final: 0.8070 (mmm) REVERT: E 272 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7657 (mtmm) REVERT: E 336 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7900 (t80) REVERT: E 370 ARG cc_start: 0.7990 (tmt-80) cc_final: 0.7591 (tmt-80) REVERT: E 402 TRP cc_start: 0.6619 (t-100) cc_final: 0.6209 (t-100) REVERT: F 151 LYS cc_start: 0.6237 (mtpt) cc_final: 0.5442 (ptmt) REVERT: F 180 MET cc_start: 0.6193 (tmm) cc_final: 0.5944 (tmm) REVERT: F 183 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.4838 (m-80) REVERT: F 247 MET cc_start: 0.7781 (ptp) cc_final: 0.7539 (ptp) REVERT: F 364 HIS cc_start: 0.6120 (OUTLIER) cc_final: 0.5468 (t70) REVERT: F 398 ASN cc_start: 0.6170 (p0) cc_final: 0.5344 (t0) outliers start: 58 outliers final: 45 residues processed: 293 average time/residue: 0.2040 time to fit residues: 90.7479 Evaluate side-chains 289 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 238 THR Chi-restraints excluded: chain A residue 264 LYS 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 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 238 THR 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 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 291 HIS 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 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 316 THR Chi-restraints excluded: chain D residue 384 MET 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 336 PHE 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 364 HIS 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 11 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.209502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134813 restraints weight = 17063.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138936 restraints weight = 10196.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140041 restraints weight = 7901.752| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13638 Z= 0.160 Angle : 0.605 14.612 18600 Z= 0.317 Chirality : 0.040 0.187 2040 Planarity : 0.004 0.041 2250 Dihedral : 4.254 20.068 1740 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 4.36 % Allowed : 24.69 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1572 helix: 1.96 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.50 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 199 HIS 0.007 0.001 HIS C 364 PHE 0.020 0.001 PHE D 201 TYR 0.014 0.001 TYR A 158 ARG 0.002 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.04809 ( 659) hydrogen bonds : angle 3.27313 ( 1977) SS BOND : bond 0.00443 ( 6) SS BOND : angle 0.96127 ( 12) covalent geometry : bond 0.00379 (13632) covalent geometry : angle 0.60497 (18588) *********************** 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 314 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 251 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7763 (mm-30) REVERT: A 347 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7243 (pt) REVERT: B 264 LYS cc_start: 0.6015 (tttp) cc_final: 0.5559 (mppt) REVERT: C 384 MET cc_start: 0.6659 (mmm) cc_final: 0.6203 (mtt) REVERT: C 393 ASN cc_start: 0.7715 (p0) cc_final: 0.7478 (p0) REVERT: D 209 MET cc_start: 0.8654 (mmm) cc_final: 0.8242 (mmm) REVERT: D 215 TRP cc_start: 0.8550 (t-100) cc_final: 0.8093 (t-100) REVERT: D 370 ARG cc_start: 0.7371 (ptm-80) cc_final: 0.7133 (ptm-80) REVERT: D 399 GLU cc_start: 0.5916 (pm20) cc_final: 0.5525 (pm20) REVERT: D 402 TRP cc_start: 0.8168 (t-100) cc_final: 0.7541 (t-100) REVERT: E 160 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: E 205 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7225 (mm-30) REVERT: E 209 MET cc_start: 0.8523 (mmp) cc_final: 0.8069 (mmp) REVERT: E 336 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7970 (t80) REVERT: E 370 ARG cc_start: 0.7956 (tmt-80) cc_final: 0.7330 (tmt-80) REVERT: E 402 TRP cc_start: 0.6812 (t-100) cc_final: 0.6410 (t-100) REVERT: F 151 LYS cc_start: 0.6545 (mtpt) cc_final: 0.5694 (ptmt) REVERT: F 176 ARG cc_start: 0.8394 (mmp-170) cc_final: 0.8189 (mmp80) REVERT: F 180 MET cc_start: 0.6224 (tmm) cc_final: 0.5952 (tmm) REVERT: F 183 TYR cc_start: 0.5887 (OUTLIER) cc_final: 0.4641 (m-80) REVERT: F 364 HIS cc_start: 0.6038 (OUTLIER) cc_final: 0.5434 (t70) REVERT: F 398 ASN cc_start: 0.6412 (p0) cc_final: 0.5643 (t0) outliers start: 63 outliers final: 52 residues processed: 296 average time/residue: 0.2082 time to fit residues: 93.2780 Evaluate side-chains 298 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 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 264 LYS 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 395 THR 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 238 THR 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 312 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER 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 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 316 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 160 PHE 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 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 199 TRP 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 332 LEU Chi-restraints excluded: chain F residue 364 HIS 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 131 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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** ** 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 = 0.4402 r_free = 0.4402 target = 0.208784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137636 restraints weight = 16809.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138351 restraints weight = 10659.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138073 restraints weight = 8736.227| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13638 Z= 0.157 Angle : 0.625 15.789 18600 Z= 0.326 Chirality : 0.041 0.188 2040 Planarity : 0.004 0.041 2250 Dihedral : 4.337 20.051 1740 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 4.22 % Allowed : 25.10 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1572 helix: 1.89 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.52 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 199 HIS 0.005 0.001 HIS C 291 PHE 0.022 0.001 PHE D 201 TYR 0.017 0.001 TYR E 158 ARG 0.004 0.000 ARG F 243 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 659) hydrogen bonds : angle 3.30222 ( 1977) SS BOND : bond 0.00437 ( 6) SS BOND : angle 0.93985 ( 12) covalent geometry : bond 0.00372 (13632) covalent geometry : angle 0.62431 (18588) *********************** 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 309 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 248 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 181 GLN cc_start: 0.8269 (pp30) cc_final: 0.7988 (pp30) REVERT: B 264 LYS cc_start: 0.6288 (tttp) cc_final: 0.5631 (mppt) REVERT: C 384 MET cc_start: 0.6916 (mmm) cc_final: 0.6443 (mtt) REVERT: D 180 MET cc_start: 0.4939 (ptm) cc_final: 0.4554 (mmt) REVERT: D 209 MET cc_start: 0.8634 (mmm) cc_final: 0.8221 (mmm) REVERT: D 215 TRP cc_start: 0.8576 (t-100) cc_final: 0.8186 (t-100) REVERT: D 370 ARG cc_start: 0.7367 (ptm-80) cc_final: 0.7138 (ptm-80) REVERT: D 399 GLU cc_start: 0.5611 (pm20) cc_final: 0.5164 (pm20) REVERT: D 402 TRP cc_start: 0.8124 (t-100) cc_final: 0.7527 (t-100) REVERT: E 160 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: E 209 MET cc_start: 0.8565 (mmp) cc_final: 0.8114 (mmp) REVERT: E 336 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7969 (t80) REVERT: E 370 ARG cc_start: 0.7957 (tmt-80) cc_final: 0.7276 (tmt-80) REVERT: F 151 LYS cc_start: 0.6572 (mtpt) cc_final: 0.5635 (pttp) REVERT: F 180 MET cc_start: 0.6347 (tmm) cc_final: 0.6050 (tmm) REVERT: F 183 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.4490 (m-80) REVERT: F 364 HIS cc_start: 0.6001 (OUTLIER) cc_final: 0.5391 (t70) REVERT: F 398 ASN cc_start: 0.6299 (p0) cc_final: 0.5422 (t0) outliers start: 61 outliers final: 52 residues processed: 290 average time/residue: 0.2110 time to fit residues: 91.8166 Evaluate side-chains 297 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 218 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 264 LYS 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 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 238 THR 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 312 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER 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 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 316 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 160 PHE 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 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 199 TRP 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 364 HIS 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 108 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 113 optimal weight: 0.0970 chunk 53 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 23 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.209920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139404 restraints weight = 16723.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139430 restraints weight = 10622.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140055 restraints weight = 8799.158| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4067 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= 0.134 Angle : 0.612 15.411 18600 Z= 0.321 Chirality : 0.040 0.191 2040 Planarity : 0.004 0.040 2250 Dihedral : 4.236 19.536 1740 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.01 % Allowed : 25.38 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1572 helix: 1.96 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP E 402 HIS 0.005 0.001 HIS C 291 PHE 0.022 0.001 PHE D 333 TYR 0.015 0.001 TYR E 158 ARG 0.002 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 659) hydrogen bonds : angle 3.25358 ( 1977) SS BOND : bond 0.00408 ( 6) SS BOND : angle 0.92783 ( 12) covalent geometry : bond 0.00309 (13632) covalent geometry : angle 0.61152 (18588) ********************** 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 305 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7770 (mm-30) REVERT: A 181 GLN cc_start: 0.8252 (pp30) cc_final: 0.7951 (pp30) REVERT: A 347 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7185 (pt) REVERT: B 264 LYS cc_start: 0.6222 (tttp) cc_final: 0.5621 (mppt) REVERT: C 384 MET cc_start: 0.6628 (mmm) cc_final: 0.6228 (mtt) REVERT: D 180 MET cc_start: 0.4919 (ptm) cc_final: 0.4645 (mmt) REVERT: D 209 MET cc_start: 0.8512 (mmm) cc_final: 0.8121 (mmm) REVERT: D 215 TRP cc_start: 0.8592 (t-100) cc_final: 0.8226 (t-100) REVERT: D 370 ARG cc_start: 0.7374 (ptm-80) cc_final: 0.7173 (ptm-80) REVERT: D 399 GLU cc_start: 0.5457 (pm20) cc_final: 0.5049 (pm20) REVERT: D 402 TRP cc_start: 0.8041 (t-100) cc_final: 0.7469 (t-100) REVERT: E 160 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: E 205 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6977 (mm-30) REVERT: E 209 MET cc_start: 0.8564 (mmp) cc_final: 0.8126 (mmp) REVERT: E 336 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.8009 (t80) REVERT: E 370 ARG cc_start: 0.7969 (tmt-80) cc_final: 0.7347 (tmt-80) REVERT: E 402 TRP cc_start: 0.6602 (t-100) cc_final: 0.6157 (t-100) REVERT: F 151 LYS cc_start: 0.6628 (mtpt) cc_final: 0.5760 (ptmt) REVERT: F 176 ARG cc_start: 0.8446 (mmp-170) cc_final: 0.8057 (mmp80) REVERT: F 180 MET cc_start: 0.6265 (tmm) cc_final: 0.5971 (tmm) REVERT: F 183 TYR cc_start: 0.5876 (OUTLIER) cc_final: 0.4571 (m-80) REVERT: F 364 HIS cc_start: 0.6019 (OUTLIER) cc_final: 0.5433 (t70) REVERT: F 398 ASN cc_start: 0.6284 (p0) cc_final: 0.5605 (t0) outliers start: 58 outliers final: 52 residues processed: 288 average time/residue: 0.2023 time to fit residues: 87.9448 Evaluate side-chains 300 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 243 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 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 395 THR Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 162 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 238 THR 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 312 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER 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 311 PHE 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 227 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 160 PHE 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 336 PHE Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 199 TRP 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 364 HIS 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 39 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 127 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.210900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140483 restraints weight = 16923.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141750 restraints weight = 9666.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141813 restraints weight = 7811.137| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4117 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= 0.124 Angle : 0.610 15.589 18600 Z= 0.318 Chirality : 0.040 0.186 2040 Planarity : 0.004 0.040 2250 Dihedral : 4.168 19.272 1740 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 3.80 % Allowed : 26.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1572 helix: 2.05 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP E 402 HIS 0.006 0.001 HIS C 291 PHE 0.022 0.001 PHE D 201 TYR 0.022 0.001 TYR D 158 ARG 0.002 0.000 ARG F 176 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 659) hydrogen bonds : angle 3.20804 ( 1977) SS BOND : bond 0.00393 ( 6) SS BOND : angle 0.84688 ( 12) covalent geometry : bond 0.00284 (13632) covalent geometry : angle 0.60959 (18588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4461.77 seconds wall clock time: 78 minutes 47.13 seconds (4727.13 seconds total)