Starting phenix.real_space_refine on Fri May 16 18:22:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ps5_17845/05_2025/8ps5_17845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps5_17845/05_2025/8ps5_17845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ps5_17845/05_2025/8ps5_17845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps5_17845/05_2025/8ps5_17845.map" model { file = "/net/cci-nas-00/data/ceres_data/8ps5_17845/05_2025/8ps5_17845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps5_17845/05_2025/8ps5_17845.cif" } resolution = 2.84 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 78 5.49 5 S 40 5.16 5 C 9276 2.51 5 N 2550 2.21 5 O 2942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14886 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3324 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 15, 'TRANS': 392} Chain: "B" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3324 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 15, 'TRANS': 392} Chain: "C" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3302 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Chain: "D" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3302 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 817 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 817 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Time building chain proxies: 9.47, per 1000 atoms: 0.64 Number of scatterers: 14886 At special positions: 0 Unit cell: (97.5, 89.7, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 78 15.00 O 2942 8.00 N 2550 7.00 C 9276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 45.6% alpha, 14.9% beta 38 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'A' and resid 23 through 33 removed outlier: 4.353A pdb=" N TRP A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 removed outlier: 3.817A pdb=" N PHE A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.512A pdb=" N ARG A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.724A pdb=" N LYS A 193 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 221 Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 305 through 326 removed outlier: 3.683A pdb=" N GLY A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 391 through 408 removed outlier: 3.622A pdb=" N GLY A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 34 removed outlier: 4.028A pdb=" N TRP B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 4.332A pdb=" N PHE B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.817A pdb=" N ARG B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 148 through 168 Processing helix chain 'B' and resid 172 through 189 Processing helix chain 'B' and resid 195 through 221 Processing helix chain 'B' and resid 225 through 234 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 305 through 326 removed outlier: 3.617A pdb=" N GLY B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'B' and resid 369 through 381 Processing helix chain 'B' and resid 391 through 408 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.033A pdb=" N VAL C 108 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 148 through 164 removed outlier: 3.527A pdb=" N VAL C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 183 removed outlier: 3.791A pdb=" N ARG C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 removed outlier: 3.737A pdb=" N LEU C 202 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 224 removed outlier: 3.586A pdb=" N LEU C 224 " --> pdb=" O LYS C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 225 through 241 removed outlier: 3.505A pdb=" N LEU C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 4.660A pdb=" N THR C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 324 Processing helix chain 'C' and resid 326 through 337 removed outlier: 3.503A pdb=" N GLU C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 381 removed outlier: 3.620A pdb=" N GLU C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 378 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS C 380 " --> pdb=" O PHE C 376 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 381 " --> pdb=" O GLU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 408 removed outlier: 3.635A pdb=" N GLY C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 34 Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.920A pdb=" N PHE D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 118 removed outlier: 4.223A pdb=" N ARG D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 148 through 168 Processing helix chain 'D' and resid 171 through 189 removed outlier: 3.503A pdb=" N ARG D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 221 Processing helix chain 'D' and resid 225 through 234 Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 305 through 337 removed outlier: 3.552A pdb=" N GLY D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 381 removed outlier: 3.607A pdb=" N ARG D 381 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 6.603A pdb=" N VAL A 11 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 64 " --> pdb=" O TYR A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 255 removed outlier: 4.850A pdb=" N ILE A 245 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP A 274 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 247 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 272 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU A 249 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE A 270 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 12.285A pdb=" N ILE A 268 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N VAL A 284 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 270 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA A 354 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU A 390 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE A 356 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.601A pdb=" N GLN B 3 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET B 13 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASN B 67 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N TYR B 15 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER B 65 " --> pdb=" O TYR B 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AA6, first strand: chain 'B' and resid 244 through 255 removed outlier: 6.414A pdb=" N VAL B 273 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 247 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 271 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU B 249 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASP B 269 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL B 251 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE B 267 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 253 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN B 265 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 12.087A pdb=" N ILE B 268 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N VAL B 284 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 270 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 354 " --> pdb=" O ASP B 388 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU B 390 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE B 356 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 36 through 38 Processing sheet with id=AA9, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.720A pdb=" N THR C 70 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 244 through 255 removed outlier: 4.923A pdb=" N ILE C 245 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP C 274 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C 247 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU C 272 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 249 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 270 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 12.151A pdb=" N ILE C 268 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N VAL C 284 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE C 270 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 354 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU C 390 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 356 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 15 removed outlier: 6.381A pdb=" N VAL D 11 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 35 through 38 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.355A pdb=" N LEU D 90 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 244 through 255 removed outlier: 6.648A pdb=" N VAL D 273 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 247 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA D 271 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU D 249 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP D 269 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL D 251 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE D 267 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 253 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN D 265 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 12.348A pdb=" N ILE D 268 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N VAL D 284 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE D 270 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA D 354 " --> pdb=" O ASP D 388 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU D 390 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE D 356 " --> pdb=" O LEU D 390 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3528 1.33 - 1.45: 3341 1.45 - 1.57: 8240 1.57 - 1.69: 157 1.69 - 1.81: 72 Bond restraints: 15338 Sorted by residual: bond pdb=" N GLY D 69 " pdb=" CA GLY D 69 " ideal model delta sigma weight residual 1.446 1.477 -0.031 9.70e-03 1.06e+04 1.00e+01 bond pdb=" N ASP B 169 " pdb=" CA ASP B 169 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.58e+00 bond pdb=" N LYS A 221 " pdb=" CA LYS A 221 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.55e+00 bond pdb=" N ILE D 91 " pdb=" CA ILE D 91 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.39e+00 bond pdb=" N VAL D 89 " pdb=" CA VAL D 89 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.19e-02 7.06e+03 9.37e+00 ... (remaining 15333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 20415 2.35 - 4.69: 560 4.69 - 7.04: 73 7.04 - 9.39: 14 9.39 - 11.73: 6 Bond angle restraints: 21068 Sorted by residual: angle pdb=" CA GLY D 69 " pdb=" C GLY D 69 " pdb=" O GLY D 69 " ideal model delta sigma weight residual 122.22 117.96 4.26 6.50e-01 2.37e+00 4.30e+01 angle pdb=" C ARG A 294 " pdb=" N LYS A 295 " pdb=" CA LYS A 295 " ideal model delta sigma weight residual 121.54 133.27 -11.73 1.91e+00 2.74e-01 3.77e+01 angle pdb=" C ASP B 169 " pdb=" CA ASP B 169 " pdb=" CB ASP B 169 " ideal model delta sigma weight residual 110.06 118.42 -8.36 1.44e+00 4.82e-01 3.37e+01 angle pdb=" C SER C 39 " pdb=" N ARG C 40 " pdb=" CA ARG C 40 " ideal model delta sigma weight residual 121.54 132.55 -11.01 1.91e+00 2.74e-01 3.32e+01 angle pdb=" C ARG C 189 " pdb=" N LYS C 190 " pdb=" CA LYS C 190 " ideal model delta sigma weight residual 121.54 132.36 -10.82 1.91e+00 2.74e-01 3.21e+01 ... (remaining 21063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 8420 34.68 - 69.36: 678 69.36 - 104.03: 28 104.03 - 138.71: 0 138.71 - 173.39: 2 Dihedral angle restraints: 9128 sinusoidal: 4342 harmonic: 4786 Sorted by residual: dihedral pdb=" C ASP B 169 " pdb=" N ASP B 169 " pdb=" CA ASP B 169 " pdb=" CB ASP B 169 " ideal model delta harmonic sigma weight residual -122.60 -137.36 14.76 0 2.50e+00 1.60e-01 3.49e+01 dihedral pdb=" N ASP B 169 " pdb=" C ASP B 169 " pdb=" CA ASP B 169 " pdb=" CB ASP B 169 " ideal model delta harmonic sigma weight residual 122.80 135.31 -12.51 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" CA GLY D 359 " pdb=" C GLY D 359 " pdb=" N ARG D 360 " pdb=" CA ARG D 360 " ideal model delta harmonic sigma weight residual -180.00 -156.20 -23.80 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 9125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2262 0.132 - 0.263: 92 0.263 - 0.395: 2 0.395 - 0.526: 1 0.526 - 0.658: 1 Chirality restraints: 2358 Sorted by residual: chirality pdb=" CB ILE B 245 " pdb=" CA ILE B 245 " pdb=" CG1 ILE B 245 " pdb=" CG2 ILE B 245 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA ASP B 169 " pdb=" N ASP B 169 " pdb=" C ASP B 169 " pdb=" CB ASP B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CA ILE D 234 " pdb=" N ILE D 234 " pdb=" C ILE D 234 " pdb=" CB ILE D 234 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2355 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 40 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C ARG C 40 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG C 40 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C 41 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 121 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C THR B 121 " -0.048 2.00e-02 2.50e+03 pdb=" O THR B 121 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 122 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 121 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C THR A 121 " 0.043 2.00e-02 2.50e+03 pdb=" O THR A 121 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 122 " -0.014 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1723 2.76 - 3.29: 13082 3.29 - 3.83: 25806 3.83 - 4.36: 31051 4.36 - 4.90: 51078 Nonbonded interactions: 122740 Sorted by model distance: nonbonded pdb=" OD2 ASP D 255 " pdb=" OG1 THR D 264 " model vdw 2.221 3.040 nonbonded pdb=" O ARG D 113 " pdb=" CD1 LEU D 117 " model vdw 2.226 3.460 nonbonded pdb=" NZ LYS B 263 " pdb=" OP2 DG F 22 " model vdw 2.286 3.120 nonbonded pdb=" O SER D 350 " pdb=" OG SER D 350 " model vdw 2.316 3.040 nonbonded pdb=" OE1 GLU A 330 " pdb=" OH TYR C 257 " model vdw 2.338 3.040 ... (remaining 122735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 16 or resid 21 through 408)) selection = (chain 'B' and (resid 1 through 16 or resid 21 through 408)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.220 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.010 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 15338 Z= 0.326 Angle : 0.936 11.734 21068 Z= 0.575 Chirality : 0.058 0.658 2358 Planarity : 0.007 0.058 2420 Dihedral : 21.091 173.390 6032 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.49 % Allowed : 23.17 % Favored : 75.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.70 (0.17), residues: 1612 helix: -2.66 (0.13), residues: 701 sheet: -0.22 (0.35), residues: 240 loop : -1.15 (0.20), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 325 HIS 0.007 0.002 HIS D 161 PHE 0.032 0.002 PHE A 44 TYR 0.016 0.002 TYR B 244 ARG 0.013 0.001 ARG D 299 Details of bonding type rmsd hydrogen bonds : bond 0.19076 ( 697) hydrogen bonds : angle 7.73830 ( 1938) covalent geometry : bond 0.00571 (15338) covalent geometry : angle 0.93607 (21068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 1.716 Fit side-chains REVERT: A 3 GLN cc_start: 0.7912 (mt0) cc_final: 0.7467 (mt0) REVERT: A 338 LYS cc_start: 0.7996 (pttp) cc_final: 0.7469 (mttm) REVERT: A 346 CYS cc_start: 0.8350 (m) cc_final: 0.8005 (p) REVERT: B 23 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8144 (tp) REVERT: B 386 MET cc_start: 0.8970 (mmt) cc_final: 0.7594 (mmt) REVERT: C 13 MET cc_start: 0.7656 (mmt) cc_final: 0.7455 (mmt) REVERT: C 394 ASP cc_start: 0.7934 (t0) cc_final: 0.7639 (t0) REVERT: D 13 MET cc_start: 0.4157 (ptm) cc_final: 0.3871 (ppp) REVERT: D 362 GLN cc_start: 0.8289 (pt0) cc_final: 0.7840 (pm20) outliers start: 22 outliers final: 13 residues processed: 175 average time/residue: 1.3339 time to fit residues: 256.7518 Evaluate side-chains 132 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 369 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN B 45 GLN B 51 ASN C 43 ASN C 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.166995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096360 restraints weight = 16957.651| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.17 r_work: 0.2987 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 15338 Z= 0.299 Angle : 0.626 7.051 21068 Z= 0.344 Chirality : 0.046 0.264 2358 Planarity : 0.005 0.041 2420 Dihedral : 20.666 175.416 2678 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.81 % Allowed : 22.02 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.19), residues: 1612 helix: -0.14 (0.17), residues: 705 sheet: -0.36 (0.35), residues: 232 loop : -0.51 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 325 HIS 0.008 0.001 HIS A 161 PHE 0.024 0.002 PHE A 376 TYR 0.023 0.002 TYR B 244 ARG 0.005 0.001 ARG D 299 Details of bonding type rmsd hydrogen bonds : bond 0.04970 ( 697) hydrogen bonds : angle 4.67167 ( 1938) covalent geometry : bond 0.00739 (15338) covalent geometry : angle 0.62565 (21068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 129 time to evaluate : 1.488 Fit side-chains REVERT: A 3 GLN cc_start: 0.7402 (mt0) cc_final: 0.7026 (mt0) REVERT: B 23 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.7901 (tp) REVERT: C 126 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7068 (mm) REVERT: C 285 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7408 (mttm) REVERT: C 286 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8288 (mmtm) REVERT: D 116 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7217 (mptm) REVERT: D 175 ARG cc_start: 0.6324 (ttp-170) cc_final: 0.5785 (mtm110) REVERT: D 356 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8125 (mm) outliers start: 71 outliers final: 29 residues processed: 180 average time/residue: 1.1080 time to fit residues: 222.2357 Evaluate side-chains 148 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 31 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 143 GLN B 51 ASN B 67 ASN B 362 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.170650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100731 restraints weight = 16983.078| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.21 r_work: 0.3031 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15338 Z= 0.121 Angle : 0.485 6.201 21068 Z= 0.273 Chirality : 0.041 0.200 2358 Planarity : 0.003 0.036 2420 Dihedral : 20.348 176.996 2667 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.52 % Allowed : 23.71 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.20), residues: 1612 helix: 1.42 (0.18), residues: 703 sheet: -0.28 (0.34), residues: 242 loop : -0.30 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 325 HIS 0.003 0.001 HIS A 321 PHE 0.016 0.001 PHE A 376 TYR 0.014 0.001 TYR B 392 ARG 0.003 0.000 ARG D 299 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 697) hydrogen bonds : angle 4.15046 ( 1938) covalent geometry : bond 0.00276 (15338) covalent geometry : angle 0.48457 (21068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 1.483 Fit side-chains REVERT: A 388 ASP cc_start: 0.8233 (t70) cc_final: 0.7941 (t70) REVERT: B 23 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.7968 (tp) REVERT: B 295 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7682 (ttpp) REVERT: C 136 LYS cc_start: 0.7385 (tttp) cc_final: 0.7165 (tttp) REVERT: D 13 MET cc_start: 0.5823 (ppp) cc_final: 0.3956 (ptt) REVERT: D 68 PHE cc_start: 0.5596 (OUTLIER) cc_final: 0.4652 (m-80) REVERT: D 245 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7890 (mp) REVERT: D 274 ASP cc_start: 0.8573 (p0) cc_final: 0.8081 (p0) REVERT: D 356 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8062 (mm) REVERT: D 381 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7540 (mtt90) outliers start: 52 outliers final: 15 residues processed: 158 average time/residue: 1.1622 time to fit residues: 204.5715 Evaluate side-chains 127 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 57 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 69 optimal weight: 0.0570 chunk 164 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN B 51 ASN B 67 ASN C 321 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.169603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099520 restraints weight = 16962.833| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.18 r_work: 0.3041 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15338 Z= 0.138 Angle : 0.489 7.633 21068 Z= 0.272 Chirality : 0.041 0.222 2358 Planarity : 0.003 0.032 2420 Dihedral : 20.193 177.064 2665 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.18 % Allowed : 23.98 % Favored : 72.83 % 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: 1.19 (0.21), residues: 1612 helix: 2.07 (0.19), residues: 704 sheet: -0.29 (0.35), residues: 228 loop : -0.12 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 325 HIS 0.005 0.001 HIS D 120 PHE 0.014 0.001 PHE A 376 TYR 0.013 0.001 TYR B 392 ARG 0.002 0.000 ARG D 299 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 697) hydrogen bonds : angle 3.98476 ( 1938) covalent geometry : bond 0.00327 (15338) covalent geometry : angle 0.48851 (21068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 1.505 Fit side-chains REVERT: A 79 PRO cc_start: 0.8233 (Cg_exo) cc_final: 0.7911 (Cg_endo) REVERT: A 388 ASP cc_start: 0.8269 (t70) cc_final: 0.7981 (t70) REVERT: B 23 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.7975 (tp) REVERT: B 295 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7720 (ttpp) REVERT: C 126 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7059 (mm) REVERT: C 136 LYS cc_start: 0.7465 (tttp) cc_final: 0.7223 (tttp) REVERT: C 285 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7251 (mttm) REVERT: D 13 MET cc_start: 0.5755 (ppp) cc_final: 0.4975 (ppp) REVERT: D 68 PHE cc_start: 0.5554 (OUTLIER) cc_final: 0.4982 (m-80) REVERT: D 245 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7911 (mp) REVERT: D 274 ASP cc_start: 0.8576 (p0) cc_final: 0.8059 (p0) REVERT: D 356 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8081 (mm) REVERT: D 381 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7568 (mtt90) outliers start: 47 outliers final: 18 residues processed: 141 average time/residue: 1.1930 time to fit residues: 186.9542 Evaluate side-chains 125 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.165941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.095338 restraints weight = 17097.561| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.15 r_work: 0.2972 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15338 Z= 0.269 Angle : 0.572 6.401 21068 Z= 0.312 Chirality : 0.045 0.223 2358 Planarity : 0.004 0.034 2420 Dihedral : 20.424 176.732 2665 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.79 % Allowed : 23.17 % Favored : 73.04 % 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: 1.10 (0.21), residues: 1612 helix: 1.87 (0.19), residues: 706 sheet: -0.44 (0.35), residues: 228 loop : 0.02 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 325 HIS 0.005 0.001 HIS A 161 PHE 0.022 0.002 PHE A 376 TYR 0.018 0.002 TYR B 244 ARG 0.004 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 697) hydrogen bonds : angle 4.17880 ( 1938) covalent geometry : bond 0.00672 (15338) covalent geometry : angle 0.57167 (21068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 110 time to evaluate : 1.618 Fit side-chains REVERT: B 1 MET cc_start: 0.6764 (tpp) cc_final: 0.6496 (tpp) REVERT: B 73 ASN cc_start: 0.8158 (t0) cc_final: 0.7827 (t0) REVERT: B 362 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: C 126 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7124 (mm) REVERT: C 136 LYS cc_start: 0.7465 (tttp) cc_final: 0.7207 (tttp) REVERT: C 285 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7272 (mttm) REVERT: C 328 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7496 (mttm) REVERT: D 13 MET cc_start: 0.5674 (ppp) cc_final: 0.4962 (ppp) REVERT: D 68 PHE cc_start: 0.5490 (OUTLIER) cc_final: 0.5039 (m-80) REVERT: D 245 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7972 (mp) REVERT: D 274 ASP cc_start: 0.8733 (p0) cc_final: 0.8311 (p0) REVERT: D 356 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8132 (mm) REVERT: D 381 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7447 (mtt90) REVERT: D 404 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7093 (mt-10) outliers start: 56 outliers final: 23 residues processed: 153 average time/residue: 1.2206 time to fit residues: 207.2087 Evaluate side-chains 136 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 119 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099569 restraints weight = 17000.049| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.17 r_work: 0.3028 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15338 Z= 0.113 Angle : 0.470 5.736 21068 Z= 0.265 Chirality : 0.041 0.171 2358 Planarity : 0.003 0.036 2420 Dihedral : 20.067 178.133 2663 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.64 % Allowed : 24.59 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.21), residues: 1612 helix: 2.47 (0.19), residues: 703 sheet: -0.39 (0.35), residues: 226 loop : 0.09 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 325 HIS 0.002 0.001 HIS D 92 PHE 0.018 0.001 PHE A 376 TYR 0.013 0.001 TYR B 392 ARG 0.002 0.000 ARG D 299 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 697) hydrogen bonds : angle 3.87246 ( 1938) covalent geometry : bond 0.00253 (15338) covalent geometry : angle 0.47025 (21068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 1.570 Fit side-chains REVERT: A 388 ASP cc_start: 0.8277 (t70) cc_final: 0.7976 (t70) REVERT: B 1 MET cc_start: 0.6994 (tpp) cc_final: 0.6734 (tpp) REVERT: C 136 LYS cc_start: 0.7698 (tttp) cc_final: 0.7475 (tttp) REVERT: D 13 MET cc_start: 0.5655 (ppp) cc_final: 0.4890 (ppp) REVERT: D 68 PHE cc_start: 0.5527 (OUTLIER) cc_final: 0.5043 (m-80) REVERT: D 245 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7922 (mp) REVERT: D 274 ASP cc_start: 0.8538 (p0) cc_final: 0.8033 (p0) REVERT: D 356 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8073 (mm) REVERT: D 381 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.6987 (mtt90) outliers start: 39 outliers final: 19 residues processed: 143 average time/residue: 1.1438 time to fit residues: 182.2980 Evaluate side-chains 123 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 162 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 88 optimal weight: 0.3980 chunk 152 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.168476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098065 restraints weight = 17063.410| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.17 r_work: 0.3021 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15338 Z= 0.153 Angle : 0.486 5.981 21068 Z= 0.272 Chirality : 0.042 0.180 2358 Planarity : 0.003 0.032 2420 Dihedral : 20.057 177.564 2663 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.91 % Allowed : 24.59 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.60 (0.21), residues: 1612 helix: 2.47 (0.19), residues: 705 sheet: -0.44 (0.35), residues: 232 loop : 0.17 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 325 HIS 0.004 0.001 HIS A 321 PHE 0.018 0.001 PHE A 376 TYR 0.020 0.001 TYR C 64 ARG 0.002 0.000 ARG A 299 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 697) hydrogen bonds : angle 3.87735 ( 1938) covalent geometry : bond 0.00371 (15338) covalent geometry : angle 0.48570 (21068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 1.572 Fit side-chains REVERT: A 388 ASP cc_start: 0.8292 (t70) cc_final: 0.7978 (t70) REVERT: B 1 MET cc_start: 0.7103 (tpp) cc_final: 0.6888 (tpp) REVERT: C 126 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7153 (mm) REVERT: C 136 LYS cc_start: 0.7752 (tttp) cc_final: 0.7529 (tttp) REVERT: C 285 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7221 (mttm) REVERT: C 286 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8253 (mttm) REVERT: D 13 MET cc_start: 0.5680 (ppp) cc_final: 0.4959 (ppp) REVERT: D 68 PHE cc_start: 0.5524 (OUTLIER) cc_final: 0.5036 (m-80) REVERT: D 245 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7927 (mp) REVERT: D 274 ASP cc_start: 0.8574 (p0) cc_final: 0.8060 (p0) REVERT: D 356 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8101 (mm) REVERT: D 381 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7582 (mtt90) REVERT: D 404 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7052 (mt-10) outliers start: 43 outliers final: 21 residues processed: 136 average time/residue: 1.2045 time to fit residues: 181.2391 Evaluate side-chains 126 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 4 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 107 optimal weight: 0.0030 chunk 152 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097443 restraints weight = 16988.089| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.15 r_work: 0.3009 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15338 Z= 0.172 Angle : 0.506 11.743 21068 Z= 0.279 Chirality : 0.042 0.186 2358 Planarity : 0.003 0.032 2420 Dihedral : 20.085 177.871 2663 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.98 % Allowed : 24.25 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.21), residues: 1612 helix: 2.44 (0.19), residues: 705 sheet: -0.50 (0.35), residues: 237 loop : 0.23 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 325 HIS 0.004 0.001 HIS C 120 PHE 0.019 0.001 PHE A 376 TYR 0.014 0.001 TYR C 181 ARG 0.003 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 697) hydrogen bonds : angle 3.90732 ( 1938) covalent geometry : bond 0.00420 (15338) covalent geometry : angle 0.50585 (21068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 1.515 Fit side-chains REVERT: A 388 ASP cc_start: 0.8301 (t70) cc_final: 0.7977 (t70) REVERT: B 1 MET cc_start: 0.7194 (tpp) cc_final: 0.6947 (tpp) REVERT: B 73 ASN cc_start: 0.8204 (t0) cc_final: 0.7877 (t0) REVERT: B 317 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7782 (mmtm) REVERT: C 126 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7159 (mm) REVERT: C 136 LYS cc_start: 0.7787 (tttp) cc_final: 0.7566 (tttp) REVERT: C 285 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7211 (mttm) REVERT: C 286 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8262 (mttp) REVERT: C 328 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7510 (mttm) REVERT: D 13 MET cc_start: 0.5621 (ppp) cc_final: 0.4886 (ppp) REVERT: D 68 PHE cc_start: 0.5463 (OUTLIER) cc_final: 0.5003 (m-80) REVERT: D 245 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7936 (mp) REVERT: D 274 ASP cc_start: 0.8573 (p0) cc_final: 0.8106 (p0) REVERT: D 356 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8109 (mm) REVERT: D 381 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7460 (mtt90) REVERT: D 404 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7050 (mt-10) outliers start: 44 outliers final: 22 residues processed: 137 average time/residue: 1.2468 time to fit residues: 188.8956 Evaluate side-chains 133 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 67 ASN D 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.168670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098119 restraints weight = 16755.789| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.09 r_work: 0.2981 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15338 Z= 0.206 Angle : 0.528 11.974 21068 Z= 0.290 Chirality : 0.043 0.194 2358 Planarity : 0.003 0.033 2420 Dihedral : 20.170 177.752 2662 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.64 % Allowed : 24.59 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.51 (0.21), residues: 1612 helix: 2.35 (0.19), residues: 705 sheet: -0.53 (0.35), residues: 237 loop : 0.21 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 325 HIS 0.004 0.001 HIS A 161 PHE 0.021 0.001 PHE A 376 TYR 0.014 0.001 TYR D 244 ARG 0.007 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 697) hydrogen bonds : angle 3.97082 ( 1938) covalent geometry : bond 0.00511 (15338) covalent geometry : angle 0.52848 (21068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 1.562 Fit side-chains REVERT: A 388 ASP cc_start: 0.8289 (t70) cc_final: 0.7848 (t70) REVERT: B 1 MET cc_start: 0.7266 (tpp) cc_final: 0.7053 (tpp) REVERT: B 73 ASN cc_start: 0.8205 (t0) cc_final: 0.7877 (t0) REVERT: B 86 ASN cc_start: 0.8296 (p0) cc_final: 0.7979 (p0) REVERT: C 126 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.7188 (mm) REVERT: C 136 LYS cc_start: 0.7782 (tttp) cc_final: 0.7559 (tttp) REVERT: C 285 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7285 (mttm) REVERT: C 286 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8325 (mttp) REVERT: C 295 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7607 (mtpt) REVERT: C 328 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7557 (mttm) REVERT: D 13 MET cc_start: 0.5642 (ppp) cc_final: 0.5345 (ppp) REVERT: D 245 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7961 (mp) REVERT: D 274 ASP cc_start: 0.8643 (p0) cc_final: 0.8181 (p0) REVERT: D 356 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8140 (mm) REVERT: D 381 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7558 (mtt90) REVERT: D 404 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7066 (mt-10) outliers start: 39 outliers final: 23 residues processed: 132 average time/residue: 1.1983 time to fit residues: 176.4214 Evaluate side-chains 128 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 67 ASN C 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.170054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099892 restraints weight = 16800.534| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.08 r_work: 0.3007 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15338 Z= 0.144 Angle : 0.499 11.603 21068 Z= 0.275 Chirality : 0.041 0.176 2358 Planarity : 0.003 0.032 2420 Dihedral : 20.056 178.179 2662 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.10 % Allowed : 25.27 % Favored : 72.63 % 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: 1.68 (0.22), residues: 1612 helix: 2.54 (0.19), residues: 704 sheet: -0.48 (0.35), residues: 237 loop : 0.25 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 325 HIS 0.003 0.001 HIS A 161 PHE 0.019 0.001 PHE A 376 TYR 0.014 0.001 TYR B 392 ARG 0.003 0.000 ARG A 299 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 697) hydrogen bonds : angle 3.88445 ( 1938) covalent geometry : bond 0.00344 (15338) covalent geometry : angle 0.49887 (21068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.584 Fit side-chains REVERT: A 388 ASP cc_start: 0.8273 (t70) cc_final: 0.7829 (t70) REVERT: B 1 MET cc_start: 0.7303 (tpp) cc_final: 0.7021 (tpp) REVERT: B 73 ASN cc_start: 0.8210 (t0) cc_final: 0.7882 (t0) REVERT: B 86 ASN cc_start: 0.8296 (p0) cc_final: 0.7981 (p0) REVERT: C 126 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7212 (mm) REVERT: C 136 LYS cc_start: 0.7804 (tttp) cc_final: 0.7521 (tttp) REVERT: C 285 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7249 (mttm) REVERT: C 286 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8347 (mttm) REVERT: C 328 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7532 (mttm) REVERT: D 13 MET cc_start: 0.5676 (ppp) cc_final: 0.5333 (ppp) REVERT: D 245 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7924 (mp) REVERT: D 274 ASP cc_start: 0.8607 (p0) cc_final: 0.8084 (p0) REVERT: D 356 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8087 (mm) REVERT: D 381 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7452 (mtt90) REVERT: D 404 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7040 (mt-10) outliers start: 31 outliers final: 21 residues processed: 125 average time/residue: 1.2673 time to fit residues: 175.9769 Evaluate side-chains 125 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.171346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101186 restraints weight = 16717.723| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.10 r_work: 0.3029 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15338 Z= 0.123 Angle : 0.480 12.140 21068 Z= 0.265 Chirality : 0.041 0.161 2358 Planarity : 0.003 0.033 2420 Dihedral : 19.904 178.407 2662 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.24 % Allowed : 25.34 % Favored : 72.43 % 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: 1.84 (0.22), residues: 1612 helix: 2.70 (0.19), residues: 704 sheet: -0.44 (0.36), residues: 227 loop : 0.31 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 325 HIS 0.002 0.001 HIS A 161 PHE 0.018 0.001 PHE A 376 TYR 0.012 0.001 TYR B 392 ARG 0.003 0.000 ARG A 299 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 697) hydrogen bonds : angle 3.78966 ( 1938) covalent geometry : bond 0.00286 (15338) covalent geometry : angle 0.48007 (21068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10757.37 seconds wall clock time: 185 minutes 53.08 seconds (11153.08 seconds total)