Starting phenix.real_space_refine on Wed Jun 11 18:34:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9y_37385/06_2025/8w9y_37385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9y_37385/06_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_37385/06_2025/8w9y_37385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9y_37385/06_2025/8w9y_37385.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9y_37385/06_2025/8w9y_37385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9y_37385/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.16, per 1000 atoms: 0.62 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: 2.86 Conformation dependent library (CDL) restraints added in 1.7 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: 1.09 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: 2.94 Time building geometry restraints manager: 3.45 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: 1.820 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 29.610 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- 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 : 1.417 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: 0.2215 time to fit residues: 93.4339 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 : 1.427 ------------------------------------------------------------------------------- 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 = 54)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156693 restraints weight = 17007.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145694 restraints weight = 19537.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141216 restraints weight = 18178.938| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 172 ILE cc_start: 0.8867 (mm) cc_final: 0.8434 (mt) REVERT: D 160 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: D 402 TRP cc_start: 0.8164 (t-100) cc_final: 0.7716 (t-100) REVERT: E 160 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7290 (t80) REVERT: E 209 MET cc_start: 0.8007 (mmp) cc_final: 0.7544 (mmp) REVERT: E 248 PHE cc_start: 0.8598 (t80) cc_final: 0.8395 (t80) REVERT: E 336 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7814 (t80) REVERT: F 192 ASP cc_start: 0.7380 (m-30) cc_final: 0.7174 (m-30) REVERT: F 314 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: F 315 TYR cc_start: 0.7000 (m-80) cc_final: 0.6523 (m-80) REVERT: F 398 ASN cc_start: 0.4653 (p0) cc_final: 0.3823 (p0) outliers start: 63 outliers final: 36 residues processed: 294 average time/residue: 0.2089 time to fit residues: 92.7413 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 : 1.454 ------------------------------------------------------------------------------- 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: 0.0870 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: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4461 r_free = 0.4461 target = 0.216477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.161705 restraints weight = 17095.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148313 restraints weight = 18445.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145475 restraints weight = 15083.225| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13638 Z= 0.122 Angle : 0.572 12.874 18600 Z= 0.299 Chirality : 0.039 0.198 2040 Planarity : 0.004 0.062 2250 Dihedral : 4.691 51.011 1744 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 3.46 % Allowed : 21.16 % Favored : 75.38 % 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: 1.97 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 402 HIS 0.005 0.001 HIS C 291 PHE 0.045 0.001 PHE E 277 TYR 0.019 0.001 TYR E 158 ARG 0.003 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 659) hydrogen bonds : angle 3.33104 ( 1977) SS BOND : bond 0.00279 ( 6) SS BOND : angle 0.64981 ( 12) covalent geometry : bond 0.00276 (13632) covalent geometry : angle 0.57212 (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: 50 poor density : 262 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8295 (tpp) cc_final: 0.8045 (tpp) REVERT: B 271 GLU cc_start: 0.7850 (tp30) cc_final: 0.7618 (tp30) REVERT: B 343 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7734 (mm-30) REVERT: C 172 ILE cc_start: 0.8765 (mm) cc_final: 0.8376 (mt) REVERT: C 176 ARG cc_start: 0.8558 (mmp80) cc_final: 0.7926 (mmp80) REVERT: C 393 ASN cc_start: 0.7867 (p0) cc_final: 0.7603 (p0) REVERT: D 203 MET cc_start: 0.8341 (tpt) cc_final: 0.8110 (mmm) REVERT: D 209 MET cc_start: 0.8280 (mmm) cc_final: 0.7794 (mmm) REVERT: D 370 ARG cc_start: 0.7327 (ptm-80) cc_final: 0.7100 (ptm-80) REVERT: D 402 TRP cc_start: 0.8279 (t-100) cc_final: 0.7732 (t-100) REVERT: E 160 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7267 (t80) REVERT: E 191 LEU cc_start: 0.6343 (mm) cc_final: 0.5811 (mm) REVERT: E 209 MET cc_start: 0.8333 (mmp) cc_final: 0.7891 (mmp) REVERT: E 336 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7874 (t80) REVERT: F 183 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.5039 (m-80) REVERT: F 398 ASN cc_start: 0.4962 (p0) cc_final: 0.4366 (p0) outliers start: 50 outliers final: 25 residues processed: 292 average time/residue: 0.2095 time to fit residues: 92.6588 Evaluate side-chains 270 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 99 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 HIS C 398 ASN F 174 HIS ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.214468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157452 restraints weight = 16829.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148217 restraints weight = 17973.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145028 restraints weight = 13393.561| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13638 Z= 0.131 Angle : 0.574 12.470 18600 Z= 0.301 Chirality : 0.039 0.181 2040 Planarity : 0.004 0.055 2250 Dihedral : 4.468 50.747 1742 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.15 % Allowed : 21.51 % Favored : 74.34 % 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: 0.17 (0.22), residues: 1572 helix: 2.02 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.62 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 402 HIS 0.008 0.001 HIS A 174 PHE 0.025 0.001 PHE D 201 TYR 0.017 0.001 TYR E 158 ARG 0.003 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 659) hydrogen bonds : angle 3.27836 ( 1977) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.66949 ( 12) covalent geometry : bond 0.00302 (13632) covalent geometry : angle 0.57399 (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 318 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 258 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 GLN cc_start: 0.8180 (pp30) cc_final: 0.7517 (mm-40) REVERT: B 271 GLU cc_start: 0.7931 (tp30) cc_final: 0.7652 (tp30) REVERT: B 343 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7714 (mm-30) REVERT: C 172 ILE cc_start: 0.8778 (mm) cc_final: 0.8489 (mt) REVERT: C 176 ARG cc_start: 0.8425 (mmp80) cc_final: 0.7857 (mmp80) REVERT: C 370 ARG cc_start: 0.6192 (ptt-90) cc_final: 0.5716 (ptt90) REVERT: C 384 MET cc_start: 0.6514 (mmm) cc_final: 0.6277 (tpp) REVERT: C 393 ASN cc_start: 0.7822 (p0) cc_final: 0.7510 (p0) REVERT: D 203 MET cc_start: 0.8298 (tpt) cc_final: 0.8094 (mmm) REVERT: D 209 MET cc_start: 0.8494 (mmm) cc_final: 0.7989 (mmm) REVERT: D 215 TRP cc_start: 0.8576 (t-100) cc_final: 0.7114 (t-100) REVERT: D 370 ARG cc_start: 0.7318 (ptm-80) cc_final: 0.7104 (ptm-80) REVERT: D 402 TRP cc_start: 0.8198 (t-100) cc_final: 0.7676 (t-100) REVERT: E 160 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: E 209 MET cc_start: 0.8390 (mmp) cc_final: 0.7949 (mmp) REVERT: E 336 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7900 (t80) REVERT: E 370 ARG cc_start: 0.7872 (tmt-80) cc_final: 0.7454 (tmt-80) REVERT: F 151 LYS cc_start: 0.6037 (mtpt) cc_final: 0.5468 (ptmt) REVERT: F 183 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.4862 (m-80) REVERT: F 275 ARG cc_start: 0.5547 (tpt170) cc_final: 0.5300 (tpt170) REVERT: F 318 ARG cc_start: 0.7233 (mmt180) cc_final: 0.6987 (mmt180) outliers start: 60 outliers final: 44 residues processed: 298 average time/residue: 0.2368 time to fit residues: 106.0319 Evaluate side-chains 290 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 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 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 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 254 VAL Chi-restraints excluded: chain D residue 316 THR 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 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 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: 10.0000 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4420 r_free = 0.4420 target = 0.211264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140212 restraints weight = 17064.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141345 restraints weight = 10422.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141135 restraints weight = 7935.823| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13638 Z= 0.142 Angle : 0.578 13.716 18600 Z= 0.304 Chirality : 0.039 0.191 2040 Planarity : 0.004 0.049 2250 Dihedral : 4.444 50.636 1742 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 4.50 % Allowed : 22.20 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.22), residues: 1572 helix: 1.98 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.58 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 402 HIS 0.006 0.001 HIS A 174 PHE 0.024 0.001 PHE D 201 TYR 0.018 0.001 TYR D 158 ARG 0.002 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 659) hydrogen bonds : angle 3.29905 ( 1977) SS BOND : bond 0.00456 ( 6) SS BOND : angle 0.65796 ( 12) covalent geometry : bond 0.00335 (13632) covalent geometry : angle 0.57753 (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 325 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7772 (mm-30) REVERT: B 180 MET cc_start: 0.7355 (mtt) cc_final: 0.7145 (mtt) REVERT: B 264 LYS cc_start: 0.8001 (mppt) cc_final: 0.7312 (tttp) REVERT: B 271 GLU cc_start: 0.7886 (tp30) cc_final: 0.7596 (tp30) REVERT: C 172 ILE cc_start: 0.8722 (mm) cc_final: 0.8404 (mt) REVERT: C 275 ARG cc_start: 0.5477 (tpt170) cc_final: 0.5234 (tpt170) REVERT: C 370 ARG cc_start: 0.6192 (ptt-90) cc_final: 0.5506 (ptt90) REVERT: C 384 MET cc_start: 0.6823 (mmm) cc_final: 0.6386 (mtt) REVERT: C 393 ASN cc_start: 0.7805 (p0) cc_final: 0.7462 (p0) REVERT: D 209 MET cc_start: 0.8639 (mmm) cc_final: 0.8113 (mmm) REVERT: D 215 TRP cc_start: 0.8577 (t-100) cc_final: 0.8074 (t-100) REVERT: D 247 MET cc_start: 0.7708 (mmt) cc_final: 0.7449 (mmp) REVERT: D 370 ARG cc_start: 0.7342 (ptm-80) cc_final: 0.7084 (ptm-80) REVERT: D 402 TRP cc_start: 0.8161 (t-100) cc_final: 0.7537 (t-100) REVERT: E 160 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: E 209 MET cc_start: 0.8399 (mmp) cc_final: 0.8040 (mmm) REVERT: E 336 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7910 (t80) REVERT: E 370 ARG cc_start: 0.7909 (tmt-80) cc_final: 0.7351 (tmt-80) REVERT: F 151 LYS cc_start: 0.6157 (mtpt) cc_final: 0.5536 (ptmt) REVERT: F 165 PHE cc_start: 0.7231 (t80) cc_final: 0.7004 (t80) REVERT: F 183 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.4693 (m-80) REVERT: F 318 ARG cc_start: 0.7191 (mmt180) cc_final: 0.6959 (mmt180) outliers start: 65 outliers final: 48 residues processed: 305 average time/residue: 0.2275 time to fit residues: 103.8267 Evaluate side-chains 291 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 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 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 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 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 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 316 THR 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 246 THR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 384 MET 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: 2.9990 chunk 132 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 144 optimal weight: 0.0030 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.210318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.140031 restraints weight = 17198.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140204 restraints weight = 11224.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139586 restraints weight = 8365.028| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13638 Z= 0.151 Angle : 0.590 14.102 18600 Z= 0.309 Chirality : 0.040 0.188 2040 Planarity : 0.004 0.044 2250 Dihedral : 4.466 50.366 1742 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 4.70 % Allowed : 22.27 % Favored : 73.03 % 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: 0.15 (0.22), residues: 1572 helix: 1.97 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.57 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 402 HIS 0.005 0.001 HIS A 174 PHE 0.016 0.001 PHE B 298 TYR 0.019 0.001 TYR E 158 ARG 0.002 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 659) hydrogen bonds : angle 3.28477 ( 1977) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.61311 ( 12) covalent geometry : bond 0.00355 (13632) covalent geometry : angle 0.59047 (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 320 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 252 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7738 (mm-30) REVERT: B 264 LYS cc_start: 0.8108 (mppt) cc_final: 0.7496 (tttp) REVERT: B 271 GLU cc_start: 0.7880 (tp30) cc_final: 0.7566 (tp30) REVERT: C 172 ILE cc_start: 0.8740 (mm) cc_final: 0.8507 (mt) REVERT: C 393 ASN cc_start: 0.7946 (p0) cc_final: 0.7643 (p0) REVERT: D 160 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.7194 (m-80) REVERT: D 209 MET cc_start: 0.8553 (mmm) cc_final: 0.8083 (mmm) REVERT: D 215 TRP cc_start: 0.8532 (t-100) cc_final: 0.8113 (t-100) REVERT: D 216 LEU cc_start: 0.8659 (mm) cc_final: 0.8449 (mm) REVERT: D 247 MET cc_start: 0.7779 (mmt) cc_final: 0.7559 (mmp) REVERT: D 370 ARG cc_start: 0.7368 (ptm-80) cc_final: 0.7094 (ptm-80) REVERT: D 402 TRP cc_start: 0.8175 (t-100) cc_final: 0.7514 (t-100) REVERT: E 209 MET cc_start: 0.8389 (mmp) cc_final: 0.8006 (mmm) REVERT: E 336 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7857 (t80) REVERT: E 370 ARG cc_start: 0.7908 (tmt-80) cc_final: 0.7293 (tmt-80) REVERT: F 151 LYS cc_start: 0.6307 (mtpt) cc_final: 0.5540 (ptmt) REVERT: F 180 MET cc_start: 0.6055 (tmm) cc_final: 0.5845 (tpt) REVERT: F 183 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.4677 (m-80) REVERT: F 247 MET cc_start: 0.7952 (ptp) cc_final: 0.7704 (ptp) REVERT: F 398 ASN cc_start: 0.5763 (p0) cc_final: 0.4978 (t0) outliers start: 68 outliers final: 54 residues processed: 301 average time/residue: 0.2072 time to fit residues: 95.6045 Evaluate side-chains 294 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 237 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 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 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 313 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 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 364 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 254 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 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 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 396 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 90 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 153 optimal weight: 0.0050 chunk 61 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.212861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.143130 restraints weight = 17066.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143062 restraints weight = 10451.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143506 restraints weight = 8721.405| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3501 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= 0.117 Angle : 0.575 14.978 18600 Z= 0.300 Chirality : 0.039 0.184 2040 Planarity : 0.004 0.042 2250 Dihedral : 4.171 19.136 1740 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.87 % Allowed : 23.79 % Favored : 72.34 % 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: 0.33 (0.22), residues: 1572 helix: 2.15 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.55 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 402 HIS 0.005 0.001 HIS A 174 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 0.04103 ( 659) hydrogen bonds : angle 3.18052 ( 1977) SS BOND : bond 0.00586 ( 6) SS BOND : angle 1.58833 ( 12) covalent geometry : bond 0.00264 (13632) covalent geometry : angle 0.57393 (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 310 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 254 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7739 (mm-30) REVERT: A 264 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.6123 (mptt) REVERT: A 347 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7330 (pt) REVERT: B 264 LYS cc_start: 0.8049 (mppt) cc_final: 0.7508 (tttp) REVERT: B 271 GLU cc_start: 0.7867 (tp30) cc_final: 0.7536 (tp30) REVERT: B 343 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7531 (mm-30) REVERT: C 172 ILE cc_start: 0.8807 (mm) cc_final: 0.8575 (mt) REVERT: C 192 ASP cc_start: 0.7192 (m-30) cc_final: 0.6970 (m-30) REVERT: C 384 MET cc_start: 0.6532 (mmm) cc_final: 0.6008 (mtt) REVERT: C 393 ASN cc_start: 0.7677 (p0) cc_final: 0.7425 (p0) REVERT: D 209 MET cc_start: 0.8592 (mmm) cc_final: 0.8169 (mmm) REVERT: D 215 TRP cc_start: 0.8538 (t-100) cc_final: 0.8141 (t-100) REVERT: D 216 LEU cc_start: 0.8624 (mm) cc_final: 0.8401 (mm) REVERT: D 247 MET cc_start: 0.7811 (mmt) cc_final: 0.7571 (mmp) REVERT: D 370 ARG cc_start: 0.7374 (ptm-80) cc_final: 0.7103 (ptm-80) REVERT: D 402 TRP cc_start: 0.8201 (t-100) cc_final: 0.7534 (t-100) REVERT: E 160 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: E 205 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7314 (mm-30) REVERT: E 209 MET cc_start: 0.8441 (mmp) cc_final: 0.8049 (mmm) REVERT: E 272 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7655 (mtmm) REVERT: E 336 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7900 (t80) REVERT: E 370 ARG cc_start: 0.7973 (tmt-80) cc_final: 0.7320 (tmt-80) REVERT: F 151 LYS cc_start: 0.6240 (mtpt) cc_final: 0.5479 (ptmt) REVERT: F 180 MET cc_start: 0.6235 (tmm) cc_final: 0.6023 (tpt) REVERT: F 183 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.4796 (m-80) REVERT: F 247 MET cc_start: 0.8041 (ptp) cc_final: 0.7834 (ptp) REVERT: F 398 ASN cc_start: 0.5644 (p0) cc_final: 0.4864 (t0) outliers start: 56 outliers final: 44 residues processed: 293 average time/residue: 0.2098 time to fit residues: 93.9096 Evaluate side-chains 287 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 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 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 347 ILE 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 326 LEU 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 160 PHE 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 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 11 optimal weight: 0.0060 chunk 32 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.208266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131690 restraints weight = 17129.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136442 restraints weight = 9977.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139537 restraints weight = 7514.430| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3783 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= 0.177 Angle : 0.624 14.423 18600 Z= 0.327 Chirality : 0.041 0.182 2040 Planarity : 0.004 0.041 2250 Dihedral : 4.365 20.346 1740 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 4.56 % Allowed : 23.86 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.22), residues: 1572 helix: 1.86 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.55 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 402 HIS 0.006 0.001 HIS A 174 PHE 0.028 0.002 PHE A 165 TYR 0.017 0.002 TYR A 158 ARG 0.003 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.05385 ( 659) hydrogen bonds : angle 3.33771 ( 1977) SS BOND : bond 0.00422 ( 6) SS BOND : angle 1.06018 ( 12) covalent geometry : bond 0.00422 (13632) covalent geometry : angle 0.62350 (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: 66 poor density : 248 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 264 LYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5751 (mptt) REVERT: B 264 LYS cc_start: 0.7790 (mppt) cc_final: 0.7309 (tttp) REVERT: C 172 ILE cc_start: 0.8833 (mm) cc_final: 0.8572 (mt) REVERT: C 384 MET cc_start: 0.6465 (mmm) cc_final: 0.6154 (mtt) REVERT: C 393 ASN cc_start: 0.7500 (p0) cc_final: 0.7208 (p0) REVERT: D 209 MET cc_start: 0.8553 (mmm) cc_final: 0.8173 (mmm) REVERT: D 215 TRP cc_start: 0.8583 (t-100) cc_final: 0.8206 (t-100) REVERT: D 216 LEU cc_start: 0.8695 (mm) cc_final: 0.8475 (mm) REVERT: D 370 ARG cc_start: 0.7289 (ptm-80) cc_final: 0.7059 (ptm-80) REVERT: D 399 GLU cc_start: 0.5478 (pm20) cc_final: 0.5258 (pm20) REVERT: D 402 TRP cc_start: 0.8122 (t-100) cc_final: 0.7537 (t-100) REVERT: E 160 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: E 205 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7217 (mm-30) REVERT: E 209 MET cc_start: 0.8431 (mmp) cc_final: 0.7986 (mmp) REVERT: E 272 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7628 (mtmm) REVERT: E 336 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.8034 (t80) REVERT: E 370 ARG cc_start: 0.7869 (tmt-80) cc_final: 0.7319 (tmt-80) REVERT: F 151 LYS cc_start: 0.6644 (mtpt) cc_final: 0.5797 (ptmt) REVERT: F 173 VAL cc_start: 0.8780 (m) cc_final: 0.8179 (p) REVERT: F 180 MET cc_start: 0.5977 (tmm) cc_final: 0.5656 (tpt) REVERT: F 183 TYR cc_start: 0.5872 (OUTLIER) cc_final: 0.4620 (m-80) REVERT: F 248 PHE cc_start: 0.8400 (t80) cc_final: 0.8144 (t80) REVERT: F 398 ASN cc_start: 0.5631 (p0) cc_final: 0.5018 (t0) outliers start: 66 outliers final: 52 residues processed: 298 average time/residue: 0.2068 time to fit residues: 93.3657 Evaluate side-chains 295 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 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 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 347 ILE 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 312 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain 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 160 PHE Chi-restraints excluded: chain E residue 175 GLU 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 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 331 ASN 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: 7.9990 chunk 6 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** 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 = 0.4414 r_free = 0.4414 target = 0.210397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136099 restraints weight = 16857.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139297 restraints weight = 10347.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140335 restraints weight = 7693.718| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13638 Z= 0.133 Angle : 0.589 15.491 18600 Z= 0.310 Chirality : 0.040 0.180 2040 Planarity : 0.004 0.040 2250 Dihedral : 4.244 19.802 1740 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 3.87 % Allowed : 24.48 % Favored : 71.65 % 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: 0.26 (0.22), residues: 1572 helix: 2.07 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.54 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 402 HIS 0.006 0.001 HIS A 174 PHE 0.021 0.001 PHE A 165 TYR 0.013 0.001 TYR A 158 ARG 0.005 0.000 ARG F 176 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 659) hydrogen bonds : angle 3.22127 ( 1977) SS BOND : bond 0.00353 ( 6) SS BOND : angle 0.70800 ( 12) covalent geometry : bond 0.00309 (13632) covalent geometry : angle 0.58889 (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 302 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7810 (mm-30) REVERT: A 181 GLN cc_start: 0.8244 (pp30) cc_final: 0.7949 (pp30) REVERT: A 264 LYS cc_start: 0.6437 (OUTLIER) cc_final: 0.5812 (mmtm) REVERT: A 347 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7309 (pt) REVERT: B 264 LYS cc_start: 0.7953 (mppt) cc_final: 0.7415 (tttp) REVERT: B 271 GLU cc_start: 0.7617 (tp30) cc_final: 0.7361 (tp30) REVERT: C 172 ILE cc_start: 0.8729 (mm) cc_final: 0.8501 (mt) REVERT: C 199 TRP cc_start: 0.7506 (p-90) cc_final: 0.7292 (p-90) REVERT: C 384 MET cc_start: 0.6724 (mmm) cc_final: 0.6343 (mtt) REVERT: C 393 ASN cc_start: 0.7635 (p0) cc_final: 0.7399 (p0) REVERT: D 180 MET cc_start: 0.4903 (ptm) cc_final: 0.4663 (ptm) REVERT: D 209 MET cc_start: 0.8583 (mmm) cc_final: 0.8219 (mmm) REVERT: D 215 TRP cc_start: 0.8573 (t-100) cc_final: 0.8208 (t-100) REVERT: D 216 LEU cc_start: 0.8692 (mm) cc_final: 0.8467 (mm) REVERT: D 370 ARG cc_start: 0.7314 (ptm-80) cc_final: 0.7045 (ptm-80) REVERT: D 399 GLU cc_start: 0.5625 (pm20) cc_final: 0.5233 (pm20) REVERT: D 402 TRP cc_start: 0.8147 (t-100) cc_final: 0.7583 (t-100) REVERT: E 160 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: E 205 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7193 (mm-30) REVERT: E 209 MET cc_start: 0.8514 (mmp) cc_final: 0.8068 (mmp) REVERT: E 247 MET cc_start: 0.7297 (mmp) cc_final: 0.7037 (mmt) REVERT: E 336 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7950 (t80) REVERT: E 370 ARG cc_start: 0.7992 (tmt-80) cc_final: 0.7359 (tmt-80) REVERT: F 151 LYS cc_start: 0.6545 (mtpt) cc_final: 0.5701 (ptmt) REVERT: F 180 MET cc_start: 0.6265 (tmm) cc_final: 0.5809 (tpt) REVERT: F 183 TYR cc_start: 0.5801 (OUTLIER) cc_final: 0.4534 (m-80) REVERT: F 248 PHE cc_start: 0.8472 (t80) cc_final: 0.8221 (t80) REVERT: F 364 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.5359 (t70) REVERT: F 398 ASN cc_start: 0.5652 (p0) cc_final: 0.4982 (t0) outliers start: 56 outliers final: 46 residues processed: 287 average time/residue: 0.2145 time to fit residues: 93.2340 Evaluate side-chains 288 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 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 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 313 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain C residue 241 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 326 LEU 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 160 PHE 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 254 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 311 PHE 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: 0.0980 chunk 1 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.209724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134501 restraints weight = 16684.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139257 restraints weight = 9711.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142396 restraints weight = 7306.711| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13638 Z= 0.146 Angle : 0.601 14.889 18600 Z= 0.319 Chirality : 0.040 0.180 2040 Planarity : 0.004 0.040 2250 Dihedral : 4.285 19.836 1740 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.67 % Allowed : 24.69 % Favored : 71.65 % 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: 0.20 (0.22), residues: 1572 helix: 2.02 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -2.56 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 402 HIS 0.007 0.001 HIS C 364 PHE 0.022 0.001 PHE A 165 TYR 0.020 0.001 TYR D 158 ARG 0.006 0.000 ARG F 176 Details of bonding type rmsd hydrogen bonds : bond 0.04768 ( 659) hydrogen bonds : angle 3.25995 ( 1977) SS BOND : bond 0.00353 ( 6) SS BOND : angle 0.64519 ( 12) covalent geometry : bond 0.00343 (13632) covalent geometry : angle 0.60105 (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 296 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 181 GLN cc_start: 0.8178 (pp30) cc_final: 0.7861 (pp30) REVERT: A 264 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5798 (mmtm) REVERT: A 347 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7238 (pt) REVERT: B 264 LYS cc_start: 0.7693 (mppt) cc_final: 0.7239 (tttp) REVERT: C 172 ILE cc_start: 0.8722 (mm) cc_final: 0.8493 (mt) REVERT: C 199 TRP cc_start: 0.7570 (p-90) cc_final: 0.7344 (p-90) REVERT: C 274 HIS cc_start: 0.8614 (m-70) cc_final: 0.8411 (m-70) REVERT: C 384 MET cc_start: 0.6635 (mmm) cc_final: 0.6313 (mtt) REVERT: C 393 ASN cc_start: 0.7258 (p0) cc_final: 0.7049 (p0) REVERT: D 180 MET cc_start: 0.4747 (ptm) cc_final: 0.4433 (mmt) REVERT: D 209 MET cc_start: 0.8557 (mmm) cc_final: 0.8161 (mmm) REVERT: D 215 TRP cc_start: 0.8589 (t-100) cc_final: 0.8214 (t-100) REVERT: D 216 LEU cc_start: 0.8702 (mm) cc_final: 0.8472 (mm) REVERT: D 370 ARG cc_start: 0.7261 (ptm-80) cc_final: 0.7049 (ptm-80) REVERT: D 399 GLU cc_start: 0.5432 (pm20) cc_final: 0.5055 (pm20) REVERT: D 402 TRP cc_start: 0.8103 (t-100) cc_final: 0.7620 (t-100) REVERT: E 160 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: E 205 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7206 (mm-30) REVERT: E 209 MET cc_start: 0.8508 (mmp) cc_final: 0.8066 (mmp) REVERT: E 336 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7967 (t80) REVERT: E 370 ARG cc_start: 0.7953 (tmt-80) cc_final: 0.7367 (tmt-80) REVERT: F 151 LYS cc_start: 0.6468 (mtpt) cc_final: 0.5670 (ptmt) REVERT: F 180 MET cc_start: 0.5917 (tmm) cc_final: 0.5712 (tpt) REVERT: F 183 TYR cc_start: 0.5718 (OUTLIER) cc_final: 0.4419 (m-80) REVERT: F 248 PHE cc_start: 0.8512 (t80) cc_final: 0.8237 (t80) REVERT: F 364 HIS cc_start: 0.5988 (OUTLIER) cc_final: 0.5369 (t70) REVERT: F 398 ASN cc_start: 0.5848 (p0) cc_final: 0.5153 (t0) outliers start: 53 outliers final: 46 residues processed: 283 average time/residue: 0.2296 time to fit residues: 98.3651 Evaluate side-chains 286 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 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 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 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 386 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 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 326 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 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 160 PHE Chi-restraints excluded: chain E residue 175 GLU 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 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 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: 3.9990 chunk 22 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 0.0370 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.210943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.136644 restraints weight = 16848.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141415 restraints weight = 9715.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144504 restraints weight = 7309.394| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13638 Z= 0.125 Angle : 0.591 14.069 18600 Z= 0.311 Chirality : 0.040 0.183 2040 Planarity : 0.004 0.039 2250 Dihedral : 4.195 19.088 1740 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 3.53 % Allowed : 24.90 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.10 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -2.54 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 402 HIS 0.005 0.001 HIS A 174 PHE 0.017 0.001 PHE B 387 TYR 0.020 0.001 TYR D 158 ARG 0.005 0.000 ARG F 176 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 659) hydrogen bonds : angle 3.21431 ( 1977) SS BOND : bond 0.00335 ( 6) SS BOND : angle 0.61408 ( 12) covalent geometry : bond 0.00288 (13632) covalent geometry : angle 0.59136 (18588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5378.64 seconds wall clock time: 95 minutes 47.43 seconds (5747.43 seconds total)