Starting phenix.real_space_refine on Fri Jul 3 02:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eef_47955/07_2026/9eef_47955.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eef_47955/07_2026/9eef_47955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eef_47955/07_2026/9eef_47955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eef_47955/07_2026/9eef_47955.map" model { file = "/net/cci-nas-00/data/ceres_data/9eef_47955/07_2026/9eef_47955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eef_47955/07_2026/9eef_47955.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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 K 4 8.98 5 S 44 5.16 5 C 7504 2.51 5 N 1888 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11400 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2849 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 19, 'TRANS': 329} Chain breaks: 2 Chain: "B" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2849 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 19, 'TRANS': 329} Chain breaks: 2 Chain: "C" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2849 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 19, 'TRANS': 329} Chain breaks: 2 Chain: "D" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2849 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 19, 'TRANS': 329} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Time building chain proxies: 2.66, per 1000 atoms: 0.23 Number of scatterers: 11400 At special positions: 0 Unit cell: (97.11, 97.11, 112.05, 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) K 4 19.00 S 44 16.00 O 1960 8.00 N 1888 7.00 C 7504 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: 0.79 Conformation dependent library (CDL) restraints added in 420.6 milliseconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 71.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.954A pdb=" N PHE A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 removed outlier: 4.070A pdb=" N TYR A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 215 through 225 Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'A' and resid 230 through 254 removed outlier: 4.069A pdb=" N VAL A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 316 Processing helix chain 'A' and resid 319 through 325 removed outlier: 4.105A pdb=" N ARG A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.896A pdb=" N ASP A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.524A pdb=" N PHE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 370 removed outlier: 4.737A pdb=" N ILE A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.582A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 395 through 418 removed outlier: 3.725A pdb=" N GLY A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.796A pdb=" N VAL A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.739A pdb=" N VAL A 460 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.905A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.955A pdb=" N PHE B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.070A pdb=" N TYR B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 226 through 229 Processing helix chain 'B' and resid 230 through 254 removed outlier: 4.069A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 316 Processing helix chain 'B' and resid 319 through 325 removed outlier: 4.105A pdb=" N ARG B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.897A pdb=" N ASP B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 348 removed outlier: 3.525A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 370 removed outlier: 4.736A pdb=" N ILE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.582A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 394 Processing helix chain 'B' and resid 395 through 418 removed outlier: 3.726A pdb=" N GLY B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 433 Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.796A pdb=" N VAL B 440 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.738A pdb=" N VAL B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.906A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.954A pdb=" N PHE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 removed outlier: 4.070A pdb=" N TYR C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 215 through 225 Processing helix chain 'C' and resid 226 through 229 Processing helix chain 'C' and resid 230 through 254 removed outlier: 4.069A pdb=" N VAL C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 316 Processing helix chain 'C' and resid 319 through 325 removed outlier: 4.106A pdb=" N ARG C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.897A pdb=" N ASP C 332 " --> pdb=" O MET C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 348 removed outlier: 3.525A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 370 removed outlier: 4.736A pdb=" N ILE C 366 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 379 removed outlier: 3.583A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 395 through 418 removed outlier: 3.725A pdb=" N GLY C 399 " --> pdb=" O MET C 395 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 433 Processing helix chain 'C' and resid 434 through 443 removed outlier: 3.796A pdb=" N VAL C 440 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 473 removed outlier: 3.739A pdb=" N VAL C 460 " --> pdb=" O GLY C 456 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.905A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.955A pdb=" N PHE D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 removed outlier: 4.070A pdb=" N TYR D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 226 through 229 Processing helix chain 'D' and resid 230 through 254 removed outlier: 4.070A pdb=" N VAL D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 316 Processing helix chain 'D' and resid 319 through 325 removed outlier: 4.106A pdb=" N ARG D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.896A pdb=" N ASP D 332 " --> pdb=" O MET D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 348 removed outlier: 3.525A pdb=" N PHE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 370 removed outlier: 4.736A pdb=" N ILE D 366 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 379 removed outlier: 3.583A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 394 Processing helix chain 'D' and resid 395 through 418 removed outlier: 3.725A pdb=" N GLY D 399 " --> pdb=" O MET D 395 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER D 414 " --> pdb=" O ILE D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 433 Processing helix chain 'D' and resid 434 through 443 removed outlier: 3.796A pdb=" N VAL D 440 " --> pdb=" O TRP D 436 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 473 removed outlier: 3.739A pdb=" N VAL D 460 " --> pdb=" O GLY D 456 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.905A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 8.609A pdb=" N TYR A 147 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL A 107 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE A 149 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN A 109 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 146 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 141 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 113 through 118 removed outlier: 8.609A pdb=" N TYR B 147 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL B 107 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE B 149 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 109 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 146 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 141 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 118 removed outlier: 8.609A pdb=" N TYR C 147 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL C 107 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE C 149 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN C 109 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU C 146 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 141 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 113 through 118 removed outlier: 8.609A pdb=" N TYR D 147 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL D 107 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE D 149 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN D 109 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU D 146 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D 141 " --> pdb=" O GLU D 146 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1849 1.32 - 1.44: 3275 1.44 - 1.57: 6492 1.57 - 1.69: 8 1.69 - 1.81: 68 Bond restraints: 11692 Sorted by residual: bond pdb=" C LEU A 474 " pdb=" O LEU A 474 " ideal model delta sigma weight residual 1.238 1.194 0.044 1.28e-02 6.10e+03 1.17e+01 bond pdb=" C LEU D 474 " pdb=" O LEU D 474 " ideal model delta sigma weight residual 1.238 1.194 0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" C LEU C 474 " pdb=" O LEU C 474 " ideal model delta sigma weight residual 1.238 1.194 0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" C LEU B 474 " pdb=" O LEU B 474 " ideal model delta sigma weight residual 1.238 1.194 0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" N ILE C 250 " pdb=" CA ILE C 250 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.34e-02 5.57e+03 1.10e+01 ... (remaining 11687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 13891 1.63 - 3.26: 1655 3.26 - 4.88: 238 4.88 - 6.51: 48 6.51 - 8.14: 12 Bond angle restraints: 15844 Sorted by residual: angle pdb=" N VAL D 241 " pdb=" CA VAL D 241 " pdb=" CB VAL D 241 " ideal model delta sigma weight residual 111.23 119.37 -8.14 1.65e+00 3.67e-01 2.43e+01 angle pdb=" N VAL A 241 " pdb=" CA VAL A 241 " pdb=" CB VAL A 241 " ideal model delta sigma weight residual 111.23 119.37 -8.14 1.65e+00 3.67e-01 2.43e+01 angle pdb=" N VAL B 241 " pdb=" CA VAL B 241 " pdb=" CB VAL B 241 " ideal model delta sigma weight residual 111.23 119.33 -8.10 1.65e+00 3.67e-01 2.41e+01 angle pdb=" N VAL C 241 " pdb=" CA VAL C 241 " pdb=" CB VAL C 241 " ideal model delta sigma weight residual 111.23 119.31 -8.08 1.65e+00 3.67e-01 2.40e+01 angle pdb=" CA ASP A 449 " pdb=" CB ASP A 449 " pdb=" CG ASP A 449 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 ... (remaining 15839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 6110 14.51 - 29.03: 614 29.03 - 43.54: 128 43.54 - 58.05: 44 58.05 - 72.56: 12 Dihedral angle restraints: 6908 sinusoidal: 2844 harmonic: 4064 Sorted by residual: dihedral pdb=" CA GLU C 397 " pdb=" C GLU C 397 " pdb=" N LEU C 398 " pdb=" CA LEU C 398 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU B 397 " pdb=" C GLU B 397 " pdb=" N LEU B 398 " pdb=" CA LEU B 398 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU A 397 " pdb=" C GLU A 397 " pdb=" N LEU A 398 " pdb=" CA LEU A 398 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 6905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1099 0.054 - 0.108: 460 0.108 - 0.162: 167 0.162 - 0.215: 34 0.215 - 0.269: 12 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA ILE C 466 " pdb=" N ILE C 466 " pdb=" C ILE C 466 " pdb=" CB ILE C 466 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ILE B 466 " pdb=" N ILE B 466 " pdb=" C ILE B 466 " pdb=" CB ILE B 466 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE A 466 " pdb=" N ILE A 466 " pdb=" C ILE A 466 " pdb=" CB ILE A 466 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1769 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 474 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO C 475 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 475 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 475 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 474 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO B 475 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 475 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 475 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 474 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO D 475 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 475 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 475 " -0.032 5.00e-02 4.00e+02 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.99: 6142 2.99 - 3.52: 13399 3.52 - 4.06: 18850 4.06 - 4.60: 29735 4.60 - 5.14: 40446 Nonbonded interactions: 108572 Sorted by model distance: nonbonded pdb=" OH TYR A 447 " pdb=" OG1 THR D 441 " model vdw 2.448 3.040 nonbonded pdb=" OG1 THR B 441 " pdb=" OH TYR C 447 " model vdw 2.462 3.040 nonbonded pdb=" OD1 ASP C 449 " pdb=" N MET C 450 " model vdw 2.475 3.120 nonbonded pdb=" OD1 ASP A 449 " pdb=" N MET A 450 " model vdw 2.476 3.120 nonbonded pdb=" OD1 ASP D 449 " pdb=" N MET D 450 " model vdw 2.476 3.120 ... (remaining 108567 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 103 through 491) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.610 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.012 0.080 11692 Z= 0.630 Angle : 1.137 8.138 15844 Z= 0.717 Chirality : 0.068 0.269 1772 Planarity : 0.010 0.080 2004 Dihedral : 12.981 72.564 4276 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.93 % Allowed : 9.89 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.21), residues: 1372 helix: -0.81 (0.16), residues: 904 sheet: -1.54 (0.61), residues: 48 loop : -1.85 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG D 138 TYR 0.025 0.006 TYR C 161 PHE 0.029 0.006 PHE C 435 TRP 0.021 0.006 TRP B 437 HIS 0.006 0.003 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.01174 / 0.63 (11692) covalent geometry : angle 1.13722 / 0.72 (15844) hydrogen bonds : bond 0.14299 / 9.58 ( 624) hydrogen bonds : angle 6.04462 / 4.17 ( 1776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8493 (tp) cc_final: 0.8260 (tt) REVERT: A 332 ASP cc_start: 0.8115 (t70) cc_final: 0.7834 (t0) REVERT: A 367 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6675 (mmm160) REVERT: A 392 LYS cc_start: 0.7499 (ttmt) cc_final: 0.6965 (tptt) REVERT: A 395 MET cc_start: 0.7122 (ttt) cc_final: 0.6901 (ttp) REVERT: B 367 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6644 (mmm160) REVERT: B 392 LYS cc_start: 0.7493 (ttmt) cc_final: 0.6946 (tptt) REVERT: B 395 MET cc_start: 0.7099 (ttt) cc_final: 0.6851 (ttp) REVERT: C 367 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6668 (mmm160) REVERT: C 392 LYS cc_start: 0.7509 (ttmt) cc_final: 0.6961 (tptt) REVERT: C 395 MET cc_start: 0.7075 (ttt) cc_final: 0.6830 (ttp) REVERT: D 367 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6613 (mmm160) REVERT: D 392 LYS cc_start: 0.7491 (ttmt) cc_final: 0.6955 (tptt) REVERT: D 395 MET cc_start: 0.7092 (ttt) cc_final: 0.6851 (ttp) REVERT: D 420 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7563 (mt-10) REVERT: D 453 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8873 (t) outliers start: 24 outliers final: 12 residues processed: 252 average time/residue: 0.1232 time to fit residues: 41.6620 Evaluate side-chains 176 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 474 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 164 GLN A 188 GLN A 380 HIS B 124 GLN B 164 GLN B 188 GLN B 380 HIS C 124 GLN C 164 GLN C 188 GLN C 380 HIS D 124 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN D 217 GLN D 380 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.268594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.217674 restraints weight = 12153.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.223017 restraints weight = 22034.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.220924 restraints weight = 12025.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.219610 restraints weight = 10153.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.220427 restraints weight = 8520.395| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11692 Z= 0.148 Angle : 0.594 6.041 15844 Z= 0.304 Chirality : 0.041 0.134 1772 Planarity : 0.005 0.040 2004 Dihedral : 5.857 51.894 1585 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.94 % Allowed : 13.99 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1372 helix: 0.22 (0.18), residues: 884 sheet: -1.39 (0.58), residues: 48 loop : -0.84 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 313 TYR 0.008 0.001 TYR B 417 PHE 0.017 0.001 PHE C 186 TRP 0.007 0.001 TRP A 305 HIS 0.003 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (11692) covalent geometry : angle 0.59430 / 0.30 (15844) hydrogen bonds : bond 0.03845 / 2.52 ( 624) hydrogen bonds : angle 4.24271 / 2.93 ( 1776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.6977 (p0) cc_final: 0.6644 (p0) REVERT: A 186 PHE cc_start: 0.8628 (t80) cc_final: 0.8239 (t80) REVERT: A 367 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6782 (mmm160) REVERT: B 367 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6760 (mmm160) REVERT: C 132 ASP cc_start: 0.6942 (p0) cc_final: 0.6700 (p0) REVERT: C 186 PHE cc_start: 0.8616 (t80) cc_final: 0.8240 (t80) REVERT: C 367 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6754 (mmm160) REVERT: D 186 PHE cc_start: 0.8568 (t80) cc_final: 0.8254 (t80) REVERT: D 367 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6733 (mmm160) REVERT: D 453 VAL cc_start: 0.8881 (m) cc_final: 0.8513 (t) outliers start: 49 outliers final: 27 residues processed: 189 average time/residue: 0.1035 time to fit residues: 27.7555 Evaluate side-chains 163 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 chunk 78 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 67 optimal weight: 0.0870 chunk 42 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 104 optimal weight: 10.0000 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN A 188 GLN A 217 GLN A 329 ASN B 188 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN C 188 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN D 188 GLN D 329 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.248948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.205442 restraints weight = 11764.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.204073 restraints weight = 20960.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.205631 restraints weight = 17372.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.205610 restraints weight = 10728.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.206498 restraints weight = 9502.071| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11692 Z= 0.111 Angle : 0.521 5.230 15844 Z= 0.266 Chirality : 0.040 0.130 1772 Planarity : 0.004 0.042 2004 Dihedral : 4.909 53.266 1572 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.38 % Allowed : 14.31 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.23), residues: 1372 helix: 0.61 (0.18), residues: 912 sheet: 0.17 (0.59), residues: 40 loop : -0.89 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 379 TYR 0.007 0.001 TYR B 417 PHE 0.016 0.001 PHE B 186 TRP 0.007 0.001 TRP C 437 HIS 0.002 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11692) covalent geometry : angle 0.52125 / 0.27 (15844) hydrogen bonds : bond 0.03244 / 2.12 ( 624) hydrogen bonds : angle 3.84885 / 2.64 ( 1776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6781 (mmm160) REVERT: A 463 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7828 (mt) REVERT: B 132 ASP cc_start: 0.6565 (p0) cc_final: 0.6314 (p0) REVERT: B 325 ARG cc_start: 0.7259 (ttt180) cc_final: 0.7029 (tpt170) REVERT: B 367 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6791 (mmm160) REVERT: B 463 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7897 (mt) REVERT: C 132 ASP cc_start: 0.6818 (p0) cc_final: 0.6579 (p0) REVERT: C 325 ARG cc_start: 0.7239 (ttt180) cc_final: 0.7014 (tpt170) REVERT: C 367 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6760 (mmm160) REVERT: C 463 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7743 (mt) REVERT: D 325 ARG cc_start: 0.7235 (ttt180) cc_final: 0.7021 (tpt170) REVERT: D 367 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6767 (mmm160) REVERT: D 453 VAL cc_start: 0.8774 (m) cc_final: 0.8461 (t) REVERT: D 463 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7669 (mt) outliers start: 42 outliers final: 29 residues processed: 175 average time/residue: 0.1130 time to fit residues: 27.9489 Evaluate side-chains 163 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 463 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN B 188 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.266268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.215292 restraints weight = 12342.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.218472 restraints weight = 22826.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.217540 restraints weight = 13968.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.215749 restraints weight = 10568.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.216689 restraints weight = 8611.976| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11692 Z= 0.191 Angle : 0.564 5.628 15844 Z= 0.291 Chirality : 0.041 0.129 1772 Planarity : 0.005 0.044 2004 Dihedral : 4.919 52.650 1572 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.42 % Allowed : 15.27 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.23), residues: 1372 helix: 0.61 (0.18), residues: 892 sheet: -0.39 (0.69), residues: 48 loop : -0.56 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 379 TYR 0.009 0.001 TYR B 417 PHE 0.016 0.001 PHE A 224 TRP 0.004 0.001 TRP A 221 HIS 0.003 0.001 HIS D 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.19 (11692) covalent geometry : angle 0.56387 / 0.29 (15844) hydrogen bonds : bond 0.03439 / 2.25 ( 624) hydrogen bonds : angle 3.80454 / 2.61 ( 1776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 136 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6850 (mmm160) REVERT: A 392 LYS cc_start: 0.7805 (ttmt) cc_final: 0.7513 (tptt) REVERT: A 463 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7816 (mt) REVERT: B 325 ARG cc_start: 0.7329 (ttt180) cc_final: 0.7059 (tpt170) REVERT: B 367 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6838 (mmm160) REVERT: B 392 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7507 (tptt) REVERT: B 397 GLU cc_start: 0.7925 (mp0) cc_final: 0.7698 (mp0) REVERT: B 463 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7833 (mt) REVERT: C 132 ASP cc_start: 0.7039 (p0) cc_final: 0.6819 (p0) REVERT: C 325 ARG cc_start: 0.7297 (ttt180) cc_final: 0.7047 (tpt170) REVERT: C 367 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6834 (mmm160) REVERT: C 392 LYS cc_start: 0.7812 (ttmt) cc_final: 0.7515 (tptt) REVERT: C 397 GLU cc_start: 0.7917 (mp0) cc_final: 0.7709 (mp0) REVERT: D 325 ARG cc_start: 0.7362 (ttt180) cc_final: 0.7108 (tpt170) REVERT: D 367 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6805 (mmm160) REVERT: D 392 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7506 (tptt) REVERT: D 397 GLU cc_start: 0.7941 (mp0) cc_final: 0.7731 (mp0) REVERT: D 453 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8538 (t) outliers start: 55 outliers final: 40 residues processed: 178 average time/residue: 0.1219 time to fit residues: 30.1967 Evaluate side-chains 166 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 98 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.263671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.213481 restraints weight = 11918.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.216628 restraints weight = 20755.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.211822 restraints weight = 10569.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.211589 restraints weight = 7798.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.212296 restraints weight = 7208.487| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11692 Z= 0.116 Angle : 0.523 7.454 15844 Z= 0.265 Chirality : 0.039 0.159 1772 Planarity : 0.004 0.044 2004 Dihedral : 4.795 53.177 1572 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.78 % Allowed : 16.40 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1372 helix: 0.84 (0.18), residues: 908 sheet: 0.96 (0.74), residues: 40 loop : -0.55 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.009 0.001 TYR C 162 PHE 0.018 0.001 PHE C 186 TRP 0.007 0.001 TRP B 437 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (11692) covalent geometry : angle 0.52306 / 0.26 (15844) hydrogen bonds : bond 0.02971 / 1.93 ( 624) hydrogen bonds : angle 3.60066 / 2.47 ( 1776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ARG cc_start: 0.7288 (ttt180) cc_final: 0.7000 (tpt170) REVERT: A 367 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6832 (mmm160) REVERT: A 392 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7526 (tptt) REVERT: B 325 ARG cc_start: 0.7364 (ttt180) cc_final: 0.7092 (tpt170) REVERT: B 367 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6809 (mmm160) REVERT: B 392 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7510 (tptt) REVERT: B 397 GLU cc_start: 0.7832 (mp0) cc_final: 0.7536 (mp0) REVERT: C 325 ARG cc_start: 0.7285 (ttt180) cc_final: 0.7047 (tpt170) REVERT: C 367 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6805 (mmm160) REVERT: C 392 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7511 (tptt) REVERT: C 397 GLU cc_start: 0.7842 (mp0) cc_final: 0.7557 (mp0) REVERT: C 463 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7773 (mt) REVERT: D 325 ARG cc_start: 0.7339 (ttt180) cc_final: 0.7103 (tpt170) REVERT: D 367 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6789 (mmm160) REVERT: D 392 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7510 (tptt) REVERT: D 397 GLU cc_start: 0.7860 (mp0) cc_final: 0.7566 (mp0) REVERT: D 453 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8391 (t) REVERT: D 463 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7768 (mt) outliers start: 47 outliers final: 28 residues processed: 164 average time/residue: 0.1262 time to fit residues: 28.5284 Evaluate side-chains 147 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 463 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 0.0770 chunk 102 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.257533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.216672 restraints weight = 11631.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.218566 restraints weight = 21765.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.218078 restraints weight = 17632.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.217310 restraints weight = 11033.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.218338 restraints weight = 8677.399| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11692 Z= 0.122 Angle : 0.512 8.271 15844 Z= 0.260 Chirality : 0.040 0.159 1772 Planarity : 0.004 0.044 2004 Dihedral : 4.720 53.080 1572 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.54 % Allowed : 16.24 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1372 helix: 0.87 (0.18), residues: 908 sheet: 0.97 (0.76), residues: 40 loop : -0.45 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 136 TYR 0.008 0.001 TYR C 417 PHE 0.021 0.001 PHE A 186 TRP 0.005 0.001 TRP B 437 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (11692) covalent geometry : angle 0.51237 / 0.26 (15844) hydrogen bonds : bond 0.02979 / 1.92 ( 624) hydrogen bonds : angle 3.50294 / 2.40 ( 1776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6838 (mmm160) REVERT: A 392 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7542 (tptt) REVERT: A 463 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7739 (mt) REVERT: B 132 ASP cc_start: 0.6469 (p0) cc_final: 0.6230 (p0) REVERT: B 367 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6817 (mmm160) REVERT: B 392 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7543 (tptt) REVERT: B 397 GLU cc_start: 0.7769 (mp0) cc_final: 0.7478 (mp0) REVERT: B 463 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7728 (mt) REVERT: C 367 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6800 (mmm160) REVERT: C 392 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7547 (tptt) REVERT: C 397 GLU cc_start: 0.7787 (mp0) cc_final: 0.7498 (mp0) REVERT: C 463 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7713 (mt) REVERT: D 367 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6786 (mmm160) REVERT: D 392 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7547 (tptt) REVERT: D 397 GLU cc_start: 0.7759 (mp0) cc_final: 0.7463 (mp0) REVERT: D 463 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7727 (mt) outliers start: 44 outliers final: 25 residues processed: 154 average time/residue: 0.1272 time to fit residues: 27.2096 Evaluate side-chains 142 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 463 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.252883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.210806 restraints weight = 11495.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.210857 restraints weight = 22968.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.209993 restraints weight = 17007.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.202945 restraints weight = 10723.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.204156 restraints weight = 9436.785| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11692 Z= 0.154 Angle : 0.526 6.929 15844 Z= 0.268 Chirality : 0.040 0.158 1772 Planarity : 0.004 0.045 2004 Dihedral : 4.657 52.134 1568 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.78 % Allowed : 16.24 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.24), residues: 1372 helix: 0.79 (0.18), residues: 908 sheet: 1.06 (0.78), residues: 40 loop : -0.30 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 325 TYR 0.012 0.001 TYR D 162 PHE 0.021 0.001 PHE C 186 TRP 0.003 0.001 TRP C 221 HIS 0.003 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.15 (11692) covalent geometry : angle 0.52641 / 0.27 (15844) hydrogen bonds : bond 0.03085 / 2.00 ( 624) hydrogen bonds : angle 3.54003 / 2.43 ( 1776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6865 (mmm160) REVERT: A 392 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7569 (tptt) REVERT: A 463 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7882 (mt) REVERT: B 367 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6856 (mmm160) REVERT: B 392 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7597 (tptt) REVERT: B 463 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7783 (mt) REVERT: C 367 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6847 (mmm160) REVERT: C 392 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7582 (tptt) REVERT: C 463 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7780 (mt) REVERT: D 367 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6815 (mmm160) REVERT: D 392 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7557 (tptt) REVERT: D 453 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8514 (t) REVERT: D 463 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7791 (mt) outliers start: 47 outliers final: 33 residues processed: 145 average time/residue: 0.1352 time to fit residues: 26.7453 Evaluate side-chains 146 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 463 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 62 optimal weight: 0.0040 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 217 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.264763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.213803 restraints weight = 11876.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.217053 restraints weight = 22378.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.216167 restraints weight = 14371.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.215277 restraints weight = 10518.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.216398 restraints weight = 8730.874| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11692 Z= 0.104 Angle : 0.486 6.505 15844 Z= 0.245 Chirality : 0.039 0.136 1772 Planarity : 0.004 0.044 2004 Dihedral : 4.530 52.546 1568 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.05 % Allowed : 16.96 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1372 helix: 1.02 (0.18), residues: 908 sheet: 1.04 (0.76), residues: 40 loop : -0.22 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.012 0.001 TYR A 162 PHE 0.020 0.001 PHE C 186 TRP 0.008 0.001 TRP B 437 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (11692) covalent geometry : angle 0.48591 / 0.24 (15844) hydrogen bonds : bond 0.02760 / 1.78 ( 624) hydrogen bonds : angle 3.41240 / 2.33 ( 1776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.6877 (p0) cc_final: 0.6549 (p0) REVERT: A 367 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6797 (mmm160) REVERT: A 392 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7550 (tptt) REVERT: A 463 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7712 (mt) REVERT: B 367 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6796 (mmm160) REVERT: B 392 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7583 (tptt) REVERT: B 463 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7677 (mt) REVERT: C 132 ASP cc_start: 0.6863 (p0) cc_final: 0.6593 (p0) REVERT: C 367 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6798 (mmm160) REVERT: C 392 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7567 (tptt) REVERT: C 463 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7692 (mt) REVERT: D 367 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6835 (mmm160) REVERT: D 392 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7549 (tptt) REVERT: D 463 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7715 (mt) outliers start: 38 outliers final: 18 residues processed: 143 average time/residue: 0.1311 time to fit residues: 25.8839 Evaluate side-chains 130 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 463 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 109 optimal weight: 0.0170 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.263033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.211681 restraints weight = 11883.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.216111 restraints weight = 21321.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.214346 restraints weight = 10487.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.212913 restraints weight = 8892.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.213961 restraints weight = 7149.233| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11692 Z= 0.132 Angle : 0.504 6.433 15844 Z= 0.255 Chirality : 0.039 0.129 1772 Planarity : 0.004 0.045 2004 Dihedral : 4.460 51.946 1564 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.05 % Allowed : 16.64 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.24), residues: 1372 helix: 0.98 (0.18), residues: 908 sheet: 1.06 (0.76), residues: 40 loop : -0.13 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.010 0.001 TYR A 162 PHE 0.018 0.001 PHE C 186 TRP 0.004 0.001 TRP B 437 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (11692) covalent geometry : angle 0.50351 / 0.25 (15844) hydrogen bonds : bond 0.02931 / 1.90 ( 624) hydrogen bonds : angle 3.41161 / 2.34 ( 1776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.6939 (p0) cc_final: 0.6572 (p0) REVERT: A 367 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6796 (mmm160) REVERT: A 392 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7618 (tptt) REVERT: A 463 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7772 (mt) REVERT: B 132 ASP cc_start: 0.6921 (p0) cc_final: 0.6690 (p0) REVERT: B 304 ILE cc_start: 0.8785 (tp) cc_final: 0.8510 (tp) REVERT: B 367 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6805 (mmm160) REVERT: B 392 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7648 (tptt) REVERT: B 463 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7775 (mt) REVERT: C 132 ASP cc_start: 0.6807 (p0) cc_final: 0.6530 (p0) REVERT: C 367 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6816 (mmm160) REVERT: C 392 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7600 (tptt) REVERT: C 463 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7730 (mt) REVERT: D 304 ILE cc_start: 0.8795 (tp) cc_final: 0.8520 (tp) REVERT: D 367 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6799 (mmm160) REVERT: D 392 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7617 (tptt) REVERT: D 463 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7768 (mt) outliers start: 38 outliers final: 22 residues processed: 145 average time/residue: 0.1311 time to fit residues: 26.2654 Evaluate side-chains 140 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 463 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 49 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.263529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.212680 restraints weight = 11981.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.214288 restraints weight = 21913.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.213158 restraints weight = 17141.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.211734 restraints weight = 11436.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.212922 restraints weight = 9481.899| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11692 Z= 0.121 Angle : 0.509 6.615 15844 Z= 0.253 Chirality : 0.039 0.127 1772 Planarity : 0.004 0.045 2004 Dihedral : 4.444 51.771 1564 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.25 % Allowed : 17.04 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1372 helix: 1.07 (0.18), residues: 908 sheet: 1.03 (0.76), residues: 40 loop : -0.02 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 136 TYR 0.015 0.001 TYR B 162 PHE 0.018 0.001 PHE C 186 TRP 0.005 0.001 TRP B 437 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (11692) covalent geometry : angle 0.50881 / 0.25 (15844) hydrogen bonds : bond 0.02841 / 1.83 ( 624) hydrogen bonds : angle 3.38913 / 2.32 ( 1776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.6990 (p0) cc_final: 0.6650 (p0) REVERT: A 367 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6796 (mmm160) REVERT: A 392 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7604 (tptt) REVERT: A 463 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7658 (mt) REVERT: B 132 ASP cc_start: 0.6987 (p0) cc_final: 0.6774 (p0) REVERT: B 304 ILE cc_start: 0.8781 (tp) cc_final: 0.8495 (tp) REVERT: B 367 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6804 (mmm160) REVERT: B 392 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7596 (tptt) REVERT: B 463 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7819 (mt) REVERT: C 132 ASP cc_start: 0.6897 (p0) cc_final: 0.6635 (p0) REVERT: C 367 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6803 (mmm160) REVERT: C 392 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7580 (tptt) REVERT: C 463 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7800 (mt) REVERT: D 304 ILE cc_start: 0.8806 (tp) cc_final: 0.8530 (tp) REVERT: D 367 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6783 (mmm160) REVERT: D 392 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7609 (tptt) REVERT: D 463 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7722 (mt) outliers start: 28 outliers final: 19 residues processed: 140 average time/residue: 0.1334 time to fit residues: 25.6284 Evaluate side-chains 133 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 463 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.263970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.213893 restraints weight = 11987.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.218511 restraints weight = 21722.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.215255 restraints weight = 11517.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.214731 restraints weight = 9854.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.215640 restraints weight = 7991.577| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11692 Z= 0.115 Angle : 0.501 6.509 15844 Z= 0.250 Chirality : 0.039 0.126 1772 Planarity : 0.004 0.045 2004 Dihedral : 4.418 51.383 1564 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.41 % Allowed : 16.88 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1372 helix: 1.15 (0.18), residues: 908 sheet: 1.04 (0.75), residues: 40 loop : 0.05 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 136 TYR 0.013 0.001 TYR B 162 PHE 0.023 0.001 PHE D 323 TRP 0.006 0.001 TRP B 437 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.11 (11692) covalent geometry : angle 0.50102 / 0.25 (15844) hydrogen bonds : bond 0.02796 / 1.80 ( 624) hydrogen bonds : angle 3.36505 / 2.31 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1708.49 seconds wall clock time: 30 minutes 25.04 seconds (1825.04 seconds total)