Starting phenix.real_space_refine on Wed Feb 4 15:56:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eef_47955/02_2026/9eef_47955.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eef_47955/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9eef_47955/02_2026/9eef_47955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eef_47955/02_2026/9eef_47955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eef_47955/02_2026/9eef_47955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eef_47955/02_2026/9eef_47955.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.68, per 1000 atoms: 0.24 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: 0.70 Conformation dependent library (CDL) restraints added in 358.6 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: 0.32 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: 1.81 Time building geometry restraints manager: 0.95 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: 2.780 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.500 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 covalent geometry : bond 0.01174 (11692) covalent geometry : angle 1.13722 (15844) hydrogen bonds : bond 0.14299 ( 624) hydrogen bonds : angle 6.04462 ( 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 : 0.399 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: 0.1168 time to fit residues: 39.8168 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 : 0.282 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4723 r_free = 0.4723 target = 0.268668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.217440 restraints weight = 12125.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.220979 restraints weight = 23102.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.220206 restraints weight = 12808.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.219489 restraints weight = 8958.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.220807 restraints weight = 7386.125| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 0.031 11692 Z= 0.144 Angle : 0.592 5.862 15844 Z= 0.303 Chirality : 0.042 0.137 1772 Planarity : 0.005 0.040 2004 Dihedral : 5.856 51.696 1585 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.38 % Allowed : 14.15 % Favored : 82.48 % 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: -0.48 (0.22), residues: 1372 helix: 0.24 (0.18), residues: 884 sheet: -1.39 (0.58), residues: 48 loop : -1.14 (0.29), 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 0.018 0.001 PHE C 186 TRP 0.007 0.001 TRP C 437 HIS 0.003 0.001 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.00340 (11692) covalent geometry : angle 0.59233 (15844) hydrogen bonds : bond 0.03818 ( 624) hydrogen bonds : angle 4.23554 ( 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 198 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.6894 (p0) cc_final: 0.6539 (p0) REVERT: A 186 PHE cc_start: 0.8630 (t80) cc_final: 0.8266 (t80) REVERT: A 367 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6780 (mmm160) REVERT: B 367 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6767 (mmm160) REVERT: C 186 PHE cc_start: 0.8611 (t80) cc_final: 0.8303 (t80) REVERT: C 367 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6747 (mmm160) REVERT: D 367 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6738 (mmm160) REVERT: D 420 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7403 (mt-10) REVERT: D 453 VAL cc_start: 0.8892 (m) cc_final: 0.8523 (t) outliers start: 42 outliers final: 28 residues processed: 183 average time/residue: 0.1047 time to fit residues: 27.0126 Evaluate side-chains 169 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 67 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 217 GLN A 329 ASN B 188 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN D 329 ASN D 380 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.251038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.208112 restraints weight = 11897.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.209491 restraints weight = 22583.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.209381 restraints weight = 17604.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.208357 restraints weight = 11756.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.209529 restraints weight = 10066.940| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11692 Z= 0.120 Angle : 0.528 5.402 15844 Z= 0.270 Chirality : 0.040 0.130 1772 Planarity : 0.004 0.042 2004 Dihedral : 4.924 53.044 1572 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.94 % Allowed : 14.71 % Favored : 81.35 % 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: -0.04 (0.23), residues: 1372 helix: 0.55 (0.18), residues: 912 sheet: 0.23 (0.59), residues: 40 loop : -1.18 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 313 TYR 0.008 0.001 TYR D 417 PHE 0.015 0.001 PHE A 224 TRP 0.007 0.001 TRP C 437 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00278 (11692) covalent geometry : angle 0.52802 (15844) hydrogen bonds : bond 0.03408 ( 624) hydrogen bonds : angle 3.86866 ( 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 196 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.6780 (p0) cc_final: 0.6467 (p0) REVERT: A 367 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6788 (mmm160) REVERT: A 463 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7899 (mt) REVERT: B 132 ASP cc_start: 0.6515 (p0) cc_final: 0.6292 (p0) REVERT: B 325 ARG cc_start: 0.7235 (ttt180) cc_final: 0.7012 (tpt170) REVERT: B 367 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6809 (mmm160) REVERT: B 463 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7761 (mt) REVERT: C 132 ASP cc_start: 0.6561 (p0) cc_final: 0.6301 (p0) REVERT: C 325 ARG cc_start: 0.7205 (ttt180) cc_final: 0.7005 (tpt170) REVERT: C 332 ASP cc_start: 0.8057 (t70) cc_final: 0.7746 (t0) REVERT: C 367 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6767 (mmm160) REVERT: C 463 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7683 (mt) REVERT: D 132 ASP cc_start: 0.6560 (p0) cc_final: 0.6317 (p0) REVERT: D 367 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6780 (mmm160) REVERT: D 453 VAL cc_start: 0.8870 (m) cc_final: 0.8476 (t) REVERT: D 463 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7862 (mt) outliers start: 49 outliers final: 30 residues processed: 185 average time/residue: 0.0956 time to fit residues: 25.0120 Evaluate side-chains 170 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 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 303 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 426 SER 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: 7.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 217 GLN B 188 GLN C 188 GLN D 188 GLN D 217 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.255317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.208018 restraints weight = 12083.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.209795 restraints weight = 25260.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.209014 restraints weight = 16134.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.208269 restraints weight = 10884.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.211389 restraints weight = 8302.553| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 11692 Z= 0.296 Angle : 0.657 6.801 15844 Z= 0.339 Chirality : 0.045 0.132 1772 Planarity : 0.005 0.044 2004 Dihedral : 5.173 51.353 1572 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.90 % Allowed : 15.68 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.39 (0.23), residues: 1372 helix: 0.17 (0.17), residues: 916 sheet: -0.54 (0.70), residues: 48 loop : -0.97 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 325 TYR 0.011 0.002 TYR B 487 PHE 0.015 0.002 PHE C 149 TRP 0.005 0.001 TRP A 221 HIS 0.005 0.002 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00749 (11692) covalent geometry : angle 0.65682 (15844) hydrogen bonds : bond 0.03943 ( 624) hydrogen bonds : angle 4.04489 ( 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 193 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 132 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6833 (mmm160) REVERT: A 392 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7357 (tptt) REVERT: A 463 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7722 (mt) REVERT: B 325 ARG cc_start: 0.7242 (ttt180) cc_final: 0.7011 (tpt170) REVERT: B 367 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6809 (mmm160) REVERT: B 392 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7371 (tptt) REVERT: B 463 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7745 (mt) REVERT: C 325 ARG cc_start: 0.7221 (ttt180) cc_final: 0.7001 (tpt170) REVERT: C 367 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6797 (mmm160) REVERT: C 392 LYS cc_start: 0.7859 (ttmt) cc_final: 0.7393 (tptt) REVERT: C 463 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7995 (mp) REVERT: D 367 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6786 (mmm160) REVERT: D 392 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7398 (tptt) REVERT: D 453 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8702 (t) REVERT: D 463 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7839 (mp) outliers start: 61 outliers final: 42 residues processed: 172 average time/residue: 0.0965 time to fit residues: 23.3439 Evaluate side-chains 170 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 454 THR 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 454 THR 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 222 LEU 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 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 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 426 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 98 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 217 GLN B 164 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN D 217 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.260434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.208408 restraints weight = 11934.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.203626 restraints weight = 18528.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.206382 restraints weight = 13625.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.206497 restraints weight = 8039.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.212950 restraints weight = 6335.825| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2415 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= 0.138 Angle : 0.544 7.792 15844 Z= 0.275 Chirality : 0.040 0.157 1772 Planarity : 0.004 0.044 2004 Dihedral : 4.965 51.769 1572 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.94 % Allowed : 17.60 % Favored : 78.46 % 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: 0.06 (0.23), residues: 1372 helix: 0.52 (0.18), residues: 908 sheet: -0.40 (0.74), residues: 48 loop : -0.76 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.010 0.001 TYR D 162 PHE 0.016 0.001 PHE B 224 TRP 0.007 0.001 TRP B 437 HIS 0.002 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00334 (11692) covalent geometry : angle 0.54359 (15844) hydrogen bonds : bond 0.03257 ( 624) hydrogen bonds : angle 3.77110 ( 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 179 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6784 (mmm160) REVERT: A 380 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.7108 (m90) REVERT: A 392 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7564 (tptt) REVERT: B 367 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6815 (mmm160) REVERT: B 380 HIS cc_start: 0.7345 (OUTLIER) cc_final: 0.7097 (m90) REVERT: B 392 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7511 (tptt) REVERT: C 367 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6790 (mmm160) REVERT: C 380 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.7123 (m90) REVERT: C 392 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7548 (tptt) REVERT: D 367 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6776 (mmm160) REVERT: D 392 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7585 (tptt) outliers start: 49 outliers final: 32 residues processed: 170 average time/residue: 0.1061 time to fit residues: 25.1495 Evaluate side-chains 156 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 253 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 380 HIS 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 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 380 HIS Chi-restraints excluded: chain B residue 423 ASP 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 303 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 454 THR 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 303 ILE Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 423 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 10.0000 chunk 49 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4674 r_free = 0.4674 target = 0.260915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.209596 restraints weight = 11952.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.213524 restraints weight = 22694.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.212961 restraints weight = 11362.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.211249 restraints weight = 9176.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.212370 restraints weight = 7820.387| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11692 Z= 0.146 Angle : 0.547 8.264 15844 Z= 0.279 Chirality : 0.041 0.172 1772 Planarity : 0.004 0.044 2004 Dihedral : 4.895 51.783 1572 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.82 % Allowed : 16.48 % Favored : 78.70 % 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: 0.62 (0.18), residues: 908 sheet: 0.80 (0.78), residues: 40 loop : -0.77 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 136 TYR 0.010 0.001 TYR C 162 PHE 0.015 0.001 PHE C 224 TRP 0.005 0.001 TRP B 437 HIS 0.002 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00357 (11692) covalent geometry : angle 0.54690 (15844) hydrogen bonds : bond 0.03260 ( 624) hydrogen bonds : angle 3.66826 ( 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 178 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 118 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6804 (mmm160) REVERT: A 392 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7616 (tptt) REVERT: A 463 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7784 (mt) REVERT: B 132 ASP cc_start: 0.6588 (p0) cc_final: 0.6294 (p0) REVERT: B 367 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6792 (mmm160) REVERT: B 380 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6970 (m90) REVERT: B 392 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7628 (tptt) REVERT: B 463 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7781 (mt) REVERT: C 367 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6794 (mmm160) REVERT: C 380 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6969 (m90) REVERT: C 392 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7627 (tptt) REVERT: C 463 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7733 (mt) REVERT: D 132 ASP cc_start: 0.6709 (p0) cc_final: 0.6453 (p0) REVERT: D 367 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6805 (mmm160) REVERT: D 392 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7634 (tptt) REVERT: D 453 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8524 (t) REVERT: D 463 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7780 (mt) outliers start: 60 outliers final: 36 residues processed: 166 average time/residue: 0.1085 time to fit residues: 25.2148 Evaluate side-chains 157 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 110 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 366 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 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 369 VAL Chi-restraints excluded: chain B residue 380 HIS 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 301 LEU 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 371 VAL Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 454 THR 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 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 463 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.0970 chunk 130 optimal weight: 0.1980 chunk 106 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.255572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.214440 restraints weight = 11462.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.214382 restraints weight = 21683.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.213893 restraints weight = 16375.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.206428 restraints weight = 9666.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.206725 restraints weight = 7921.695| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11692 Z= 0.105 Angle : 0.504 7.578 15844 Z= 0.256 Chirality : 0.039 0.169 1772 Planarity : 0.004 0.044 2004 Dihedral : 4.715 52.576 1572 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.46 % Allowed : 17.52 % Favored : 79.02 % 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: 0.50 (0.24), residues: 1372 helix: 0.83 (0.18), residues: 908 sheet: 0.87 (0.79), residues: 40 loop : -0.65 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 313 TYR 0.008 0.001 TYR D 162 PHE 0.020 0.001 PHE C 186 TRP 0.008 0.001 TRP A 437 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00240 (11692) covalent geometry : angle 0.50351 (15844) hydrogen bonds : bond 0.02939 ( 624) hydrogen bonds : angle 3.52388 ( 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 163 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7348 (p0) cc_final: 0.7061 (p0) REVERT: A 367 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6744 (mmm160) REVERT: A 392 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7283 (tptt) REVERT: A 463 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7618 (mt) REVERT: B 367 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6718 (mmm160) REVERT: B 392 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7296 (tptt) REVERT: B 463 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7565 (mt) REVERT: C 367 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6706 (mmm160) REVERT: C 392 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7287 (tptt) REVERT: C 463 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7552 (mt) REVERT: D 132 ASP cc_start: 0.7471 (p0) cc_final: 0.7257 (p0) REVERT: D 367 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6698 (mmm160) REVERT: D 392 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7306 (tptt) REVERT: D 463 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7568 (mt) outliers start: 43 outliers final: 27 residues processed: 157 average time/residue: 0.1223 time to fit residues: 26.2515 Evaluate side-chains 141 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 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 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 454 THR 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 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 454 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 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 = 0.4663 r_free = 0.4663 target = 0.259191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.208715 restraints weight = 11842.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.210938 restraints weight = 23167.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.211175 restraints weight = 14596.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.210351 restraints weight = 9999.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.214350 restraints weight = 8098.607| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11692 Z= 0.188 Angle : 0.555 6.403 15844 Z= 0.284 Chirality : 0.041 0.141 1772 Planarity : 0.005 0.045 2004 Dihedral : 4.795 51.515 1572 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.58 % Allowed : 15.92 % Favored : 79.50 % 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: 0.32 (0.23), residues: 1372 helix: 0.64 (0.18), residues: 908 sheet: 0.94 (0.80), residues: 40 loop : -0.61 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 313 TYR 0.014 0.001 TYR D 162 PHE 0.018 0.001 PHE C 186 TRP 0.004 0.001 TRP B 221 HIS 0.003 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00471 (11692) covalent geometry : angle 0.55467 (15844) hydrogen bonds : bond 0.03252 ( 624) hydrogen bonds : angle 3.61909 ( 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 170 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 113 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6786 (mmm160) REVERT: A 380 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.7121 (m90) REVERT: A 392 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7514 (tptt) REVERT: A 463 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7836 (mt) REVERT: B 367 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6797 (mmm160) REVERT: B 392 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7441 (tptt) REVERT: B 405 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7333 (mp) REVERT: B 463 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7982 (mt) REVERT: C 367 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6785 (mmm160) REVERT: C 392 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7443 (tptt) REVERT: C 463 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7926 (mt) REVERT: D 329 ASN cc_start: 0.8450 (m110) cc_final: 0.8126 (m-40) REVERT: D 367 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6779 (mmm160) REVERT: D 392 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7502 (tptt) REVERT: D 463 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7825 (mt) outliers start: 57 outliers final: 40 residues processed: 161 average time/residue: 0.1153 time to fit residues: 25.8197 Evaluate side-chains 153 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 103 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 250 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 380 HIS 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 250 ILE 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 371 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 454 THR 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 238 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 371 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 229 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 250 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 371 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN B 217 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.263452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.212266 restraints weight = 11878.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.216790 restraints weight = 21005.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.215204 restraints weight = 12088.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.214518 restraints weight = 9112.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.215357 restraints weight = 7585.320| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2999 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= 0.108 Angle : 0.495 6.285 15844 Z= 0.251 Chirality : 0.039 0.135 1772 Planarity : 0.004 0.045 2004 Dihedral : 4.673 51.948 1572 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.78 % Allowed : 16.48 % Favored : 79.74 % 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: 0.62 (0.24), residues: 1372 helix: 0.86 (0.18), residues: 908 sheet: 1.09 (0.79), residues: 40 loop : -0.46 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 313 TYR 0.012 0.001 TYR D 162 PHE 0.023 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 covalent geometry : bond 0.00249 (11692) covalent geometry : angle 0.49546 (15844) hydrogen bonds : bond 0.02898 ( 624) hydrogen bonds : angle 3.49888 ( 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 165 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 0.392 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 367 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6837 (mmm160) REVERT: A 392 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7580 (tptt) REVERT: A 463 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7839 (mt) REVERT: B 367 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6815 (mmm160) REVERT: B 392 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7572 (tptt) REVERT: B 463 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7807 (mt) REVERT: C 367 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6805 (mmm160) REVERT: C 392 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7582 (tptt) REVERT: C 463 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7716 (mt) REVERT: D 329 ASN cc_start: 0.8452 (m110) cc_final: 0.8220 (m-40) REVERT: D 367 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6777 (mmm160) REVERT: D 392 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7592 (tptt) REVERT: D 463 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7699 (mt) outliers start: 47 outliers final: 33 residues processed: 155 average time/residue: 0.1132 time to fit residues: 24.1061 Evaluate side-chains 155 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 423 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 132 ASP 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 423 ASP Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 489 ARG 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 301 LEU 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 C residue 489 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 250 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 454 THR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 489 ARG 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: 0.8980 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4692 r_free = 0.4692 target = 0.262963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.213299 restraints weight = 11989.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.215827 restraints weight = 20841.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.208829 restraints weight = 9189.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.208557 restraints weight = 7282.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.209802 restraints weight = 5649.266| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3064 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= 0.119 Angle : 0.499 6.251 15844 Z= 0.253 Chirality : 0.040 0.128 1772 Planarity : 0.004 0.045 2004 Dihedral : 4.625 51.521 1572 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.22 % Allowed : 16.88 % Favored : 79.90 % 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: 0.75 (0.24), residues: 1372 helix: 0.93 (0.18), residues: 908 sheet: 1.14 (0.78), residues: 40 loop : -0.33 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 151 TYR 0.016 0.001 TYR A 162 PHE 0.022 0.001 PHE C 186 TRP 0.006 0.001 TRP B 437 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00288 (11692) covalent geometry : angle 0.49931 (15844) hydrogen bonds : bond 0.02951 ( 624) hydrogen bonds : angle 3.47051 ( 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 162 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.305 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 132 ASP cc_start: 0.7685 (p0) cc_final: 0.7196 (p0) REVERT: A 367 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6729 (mmm160) REVERT: A 392 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7277 (tptt) REVERT: A 463 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7661 (mt) REVERT: B 304 ILE cc_start: 0.8808 (tp) cc_final: 0.8521 (tp) REVERT: B 367 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6730 (mmm160) REVERT: B 392 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7271 (tptt) REVERT: B 463 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7687 (mt) REVERT: C 367 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6733 (mmm160) REVERT: C 392 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7255 (tptt) REVERT: C 463 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7588 (mt) REVERT: D 304 ILE cc_start: 0.8803 (tp) cc_final: 0.8541 (tp) REVERT: D 329 ASN cc_start: 0.8509 (m110) cc_final: 0.8242 (m-40) REVERT: D 367 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6698 (mmm160) REVERT: D 392 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7271 (tptt) REVERT: D 463 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7591 (mt) outliers start: 40 outliers final: 26 residues processed: 154 average time/residue: 0.1089 time to fit residues: 23.2561 Evaluate side-chains 147 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 B residue 489 ARG 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 301 LEU 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 C residue 489 ARG 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 250 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 454 THR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 489 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 329 ASN B 329 ASN ** 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 = 0.4700 r_free = 0.4700 target = 0.263473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.212908 restraints weight = 12004.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.216917 restraints weight = 20947.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.215667 restraints weight = 11538.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.214309 restraints weight = 9331.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.215334 restraints weight = 7764.897| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3148 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= 0.114 Angle : 0.496 6.194 15844 Z= 0.251 Chirality : 0.039 0.124 1772 Planarity : 0.004 0.045 2004 Dihedral : 4.466 51.327 1564 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.14 % Allowed : 16.64 % 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: 0.87 (0.24), residues: 1372 helix: 1.00 (0.18), residues: 908 sheet: 1.26 (0.76), residues: 40 loop : -0.23 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.014 0.001 TYR B 162 PHE 0.023 0.001 PHE B 186 TRP 0.006 0.001 TRP B 437 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00272 (11692) covalent geometry : angle 0.49565 (15844) hydrogen bonds : bond 0.02905 ( 624) hydrogen bonds : angle 3.44021 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.31 seconds wall clock time: 26 minutes 27.79 seconds (1587.79 seconds total)