Starting phenix.real_space_refine on Wed Mar 4 15:05:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iug_9734/03_2026/6iug_9734.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iug_9734/03_2026/6iug_9734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6iug_9734/03_2026/6iug_9734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iug_9734/03_2026/6iug_9734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iug_9734/03_2026/6iug_9734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iug_9734/03_2026/6iug_9734.map" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.000 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9225 2.51 5 N 2450 2.21 5 O 2795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14585 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2889 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.27, per 1000 atoms: 0.16 Number of scatterers: 14585 At special positions: 0 Unit cell: (93.544, 93.544, 191.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 10 15.00 Mg 5 11.99 O 2795 8.00 N 2450 7.00 C 9225 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: 1.02 Conformation dependent library (CDL) restraints added in 675.3 milliseconds 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 15 sheets defined 43.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 80 through 95 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.903A pdb=" N ARG A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.752A pdb=" N ALA A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.599A pdb=" N ILE A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.786A pdb=" N GLY A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.748A pdb=" N GLN A 356 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.281A pdb=" N VAL A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS A 373 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 114 through 128 removed outlier: 3.903A pdb=" N ARG B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.753A pdb=" N ALA B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 265 through 269 removed outlier: 3.599A pdb=" N ILE B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.786A pdb=" N GLY B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 310 through 316 Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.748A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.281A pdb=" N VAL B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS B 373 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 Processing helix chain 'C' and resid 80 through 95 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.903A pdb=" N ARG C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 148 Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.751A pdb=" N ALA C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 265 through 269 removed outlier: 3.599A pdb=" N ILE C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.785A pdb=" N GLY C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.748A pdb=" N GLN C 356 " --> pdb=" O THR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.281A pdb=" N VAL C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 373 " --> pdb=" O SER C 370 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG C 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 Processing helix chain 'D' and resid 80 through 95 Processing helix chain 'D' and resid 114 through 128 removed outlier: 3.903A pdb=" N ARG D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 148 Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.752A pdb=" N ALA D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 265 through 269 removed outlier: 3.598A pdb=" N ILE D 269 " --> pdb=" O PRO D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 292 through 297 removed outlier: 3.786A pdb=" N GLY D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 318 through 323 Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 352 through 357 removed outlier: 3.748A pdb=" N GLN D 356 " --> pdb=" O THR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 367 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.281A pdb=" N VAL D 372 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS D 373 " --> pdb=" O SER D 370 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 Processing helix chain 'E' and resid 80 through 95 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.903A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'E' and resid 183 through 196 Processing helix chain 'E' and resid 204 through 219 removed outlier: 3.752A pdb=" N ALA E 219 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 265 through 269 removed outlier: 3.598A pdb=" N ILE E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 287 Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.785A pdb=" N GLY E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 310 through 316 Processing helix chain 'E' and resid 318 through 323 Processing helix chain 'E' and resid 339 through 351 Processing helix chain 'E' and resid 352 through 357 removed outlier: 3.748A pdb=" N GLN E 356 " --> pdb=" O THR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 367 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.281A pdb=" N VAL E 372 " --> pdb=" O PRO E 369 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS E 373 " --> pdb=" O SER E 370 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG E 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.580A pdb=" N PHE A 33 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 10 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR A 108 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS A 12 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 135 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 removed outlier: 3.506A pdb=" N VAL A 37 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 39 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 180 removed outlier: 7.592A pdb=" N VAL A 300 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE A 153 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER A 302 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU A 155 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE A 299 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 34 removed outlier: 3.581A pdb=" N PHE B 33 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 135 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 56 removed outlier: 3.506A pdb=" N VAL B 37 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 39 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 178 through 180 removed outlier: 7.592A pdb=" N VAL B 300 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE B 299 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.580A pdb=" N PHE C 33 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR C 135 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.507A pdb=" N VAL C 37 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 39 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 178 through 180 removed outlier: 7.593A pdb=" N VAL C 300 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE C 153 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER C 302 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU C 155 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE C 299 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 31 through 34 removed outlier: 3.580A pdb=" N PHE D 33 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU D 10 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR D 108 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR D 135 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 55 through 56 removed outlier: 3.507A pdb=" N VAL D 37 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D 39 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 178 through 180 removed outlier: 7.593A pdb=" N VAL D 300 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE D 153 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER D 302 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU D 155 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE D 299 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 34 removed outlier: 3.580A pdb=" N PHE E 33 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU E 10 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR E 108 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR E 135 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 55 through 56 removed outlier: 3.506A pdb=" N VAL E 37 " --> pdb=" O LYS E 70 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG E 39 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 178 through 180 removed outlier: 7.592A pdb=" N VAL E 300 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE E 153 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER E 302 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU E 155 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE E 299 " --> pdb=" O VAL E 332 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4713 1.34 - 1.46: 2975 1.46 - 1.58: 7027 1.58 - 1.69: 15 1.69 - 1.81: 180 Bond restraints: 14910 Sorted by residual: bond pdb=" CB ASP E 159 " pdb=" CG ASP E 159 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" CB ASP A 159 " pdb=" CG ASP A 159 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.61e+00 bond pdb=" CB ASP B 159 " pdb=" CG ASP B 159 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.59e+00 bond pdb=" CB ASP D 159 " pdb=" CG ASP D 159 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.56e+00 bond pdb=" CB ASP C 159 " pdb=" CG ASP C 159 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.53e+00 ... (remaining 14905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 18667 1.48 - 2.96: 1258 2.96 - 4.43: 210 4.43 - 5.91: 65 5.91 - 7.39: 35 Bond angle restraints: 20235 Sorted by residual: angle pdb=" C GLN A 51 " pdb=" N LYS A 52 " pdb=" CA LYS A 52 " ideal model delta sigma weight residual 122.32 129.04 -6.72 1.76e+00 3.23e-01 1.46e+01 angle pdb=" C GLN B 51 " pdb=" N LYS B 52 " pdb=" CA LYS B 52 " ideal model delta sigma weight residual 122.32 129.01 -6.69 1.76e+00 3.23e-01 1.45e+01 angle pdb=" C GLN D 51 " pdb=" N LYS D 52 " pdb=" CA LYS D 52 " ideal model delta sigma weight residual 122.32 129.00 -6.68 1.76e+00 3.23e-01 1.44e+01 angle pdb=" C GLN C 51 " pdb=" N LYS C 52 " pdb=" CA LYS C 52 " ideal model delta sigma weight residual 122.32 128.99 -6.67 1.76e+00 3.23e-01 1.44e+01 angle pdb=" C GLN E 51 " pdb=" N LYS E 52 " pdb=" CA LYS E 52 " ideal model delta sigma weight residual 122.32 128.99 -6.67 1.76e+00 3.23e-01 1.43e+01 ... (remaining 20230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 8770 23.28 - 46.56: 170 46.56 - 69.84: 10 69.84 - 93.11: 15 93.11 - 116.39: 5 Dihedral angle restraints: 8970 sinusoidal: 3620 harmonic: 5350 Sorted by residual: dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 56.39 -116.39 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 56.38 -116.38 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 56.35 -116.35 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 8967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1589 0.051 - 0.102: 525 0.102 - 0.154: 117 0.154 - 0.205: 9 0.205 - 0.256: 10 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CB ILE C 299 " pdb=" CA ILE C 299 " pdb=" CG1 ILE C 299 " pdb=" CG2 ILE C 299 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE E 299 " pdb=" CA ILE E 299 " pdb=" CG1 ILE E 299 " pdb=" CG2 ILE E 299 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE B 299 " pdb=" CA ILE B 299 " pdb=" CG1 ILE B 299 " pdb=" CG2 ILE B 299 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2247 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 244 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO E 245 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 245 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 245 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 244 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.94e+00 pdb=" N PRO C 245 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 245 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 245 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 244 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO D 245 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 245 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 245 " 0.031 5.00e-02 4.00e+02 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 279 2.66 - 3.22: 13350 3.22 - 3.78: 23206 3.78 - 4.34: 31797 4.34 - 4.90: 50510 Nonbonded interactions: 119142 Sorted by model distance: nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.106 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.106 2.170 ... (remaining 119137 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.220 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.005 0.053 14910 Z= 0.235 Angle : 0.901 7.389 20235 Z= 0.494 Chirality : 0.055 0.256 2250 Planarity : 0.007 0.056 2580 Dihedral : 10.727 116.392 5550 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.96 % Allowed : 1.60 % Favored : 97.44 % 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: -3.83 (0.16), residues: 1845 helix: -2.48 (0.13), residues: 765 sheet: -2.07 (0.29), residues: 275 loop : -2.64 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 64 TYR 0.028 0.002 TYR D 296 PHE 0.017 0.002 PHE E 264 TRP 0.026 0.003 TRP A 342 HIS 0.013 0.002 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00508 (14910) covalent geometry : angle 0.90096 (20235) hydrogen bonds : bond 0.20530 ( 585) hydrogen bonds : angle 7.60298 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 269 time to evaluate : 0.487 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.7962 (mt0) cc_final: 0.7672 (mt0) REVERT: A 211 VAL cc_start: 0.9416 (t) cc_final: 0.8943 (t) REVERT: A 248 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8907 (mm110) REVERT: A 265 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8393 (mp10) REVERT: B 227 GLN cc_start: 0.8825 (mt0) cc_final: 0.8625 (tm-30) REVERT: B 265 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8347 (mp10) REVERT: B 327 MET cc_start: 0.6835 (tpp) cc_final: 0.6493 (tpt) REVERT: D 248 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8957 (mm110) REVERT: D 265 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8299 (mp10) REVERT: D 327 MET cc_start: 0.7040 (tpp) cc_final: 0.6676 (tpp) REVERT: E 123 GLN cc_start: 0.8717 (tt0) cc_final: 0.8383 (tm-30) REVERT: E 240 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8277 (ttpt) REVERT: E 248 GLN cc_start: 0.9337 (mm-40) cc_final: 0.9018 (mm-40) outliers start: 15 outliers final: 5 residues processed: 284 average time/residue: 0.1291 time to fit residues: 52.5928 Evaluate side-chains 164 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 240 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 HIS A 117 ASN A 298 ASN B 103 HIS B 298 ASN C 103 HIS C 298 ASN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 298 ASN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN E 356 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047391 restraints weight = 80965.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048698 restraints weight = 42608.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049572 restraints weight = 26371.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050175 restraints weight = 18132.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050567 restraints weight = 13437.702| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14910 Z= 0.155 Angle : 0.692 7.934 20235 Z= 0.339 Chirality : 0.046 0.176 2250 Planarity : 0.005 0.049 2580 Dihedral : 10.140 117.313 2089 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.69 % Allowed : 6.86 % Favored : 90.45 % 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: -2.09 (0.19), residues: 1845 helix: -0.84 (0.18), residues: 750 sheet: -1.46 (0.30), residues: 300 loop : -1.78 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 337 TYR 0.029 0.002 TYR E 225 PHE 0.008 0.001 PHE D 264 TRP 0.026 0.002 TRP C 358 HIS 0.007 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00338 (14910) covalent geometry : angle 0.69215 (20235) hydrogen bonds : bond 0.03949 ( 585) hydrogen bonds : angle 5.54892 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7862 (mtm) cc_final: 0.7630 (mmm) REVERT: A 139 GLN cc_start: 0.8176 (mt0) cc_final: 0.7884 (mt0) REVERT: A 227 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 330 LYS cc_start: 0.8638 (tttt) cc_final: 0.8404 (tttp) REVERT: B 83 ASP cc_start: 0.8317 (m-30) cc_final: 0.8074 (m-30) REVERT: B 121 MET cc_start: 0.8766 (ttp) cc_final: 0.8394 (tmm) REVERT: B 125 MET cc_start: 0.8895 (mmp) cc_final: 0.8553 (mmt) REVERT: B 192 MET cc_start: 0.7933 (mmt) cc_final: 0.7661 (mmt) REVERT: B 265 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8496 (mp10) REVERT: C 328 LYS cc_start: 0.8988 (tttt) cc_final: 0.8783 (mmtm) REVERT: E 83 ASP cc_start: 0.8345 (m-30) cc_final: 0.8123 (m-30) REVERT: E 224 ASP cc_start: 0.7780 (t0) cc_final: 0.7314 (t70) REVERT: E 230 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7381 (mm-30) REVERT: E 265 GLN cc_start: 0.8681 (mp10) cc_final: 0.8477 (mp10) outliers start: 42 outliers final: 27 residues processed: 218 average time/residue: 0.0974 time to fit residues: 33.2559 Evaluate side-chains 178 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 155 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.0270 overall best weight: 2.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 248 GLN B 117 ASN C 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047430 restraints weight = 82244.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048755 restraints weight = 43028.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049639 restraints weight = 26481.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050231 restraints weight = 18110.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050664 restraints weight = 13423.884| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14910 Z= 0.126 Angle : 0.667 8.877 20235 Z= 0.316 Chirality : 0.046 0.163 2250 Planarity : 0.004 0.038 2580 Dihedral : 9.762 120.986 2085 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.50 % Allowed : 8.21 % Favored : 89.29 % 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: -1.35 (0.20), residues: 1845 helix: -0.25 (0.19), residues: 755 sheet: -0.81 (0.32), residues: 270 loop : -1.45 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.017 0.001 TYR D 225 PHE 0.011 0.001 PHE B 264 TRP 0.014 0.002 TRP C 358 HIS 0.006 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00278 (14910) covalent geometry : angle 0.66681 (20235) hydrogen bonds : bond 0.03589 ( 585) hydrogen bonds : angle 5.25479 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.557 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 227 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 330 LYS cc_start: 0.8600 (tttt) cc_final: 0.8390 (tttp) REVERT: B 83 ASP cc_start: 0.8269 (m-30) cc_final: 0.8029 (m-30) REVERT: B 121 MET cc_start: 0.8749 (ttp) cc_final: 0.8384 (tmm) REVERT: B 125 MET cc_start: 0.8825 (mmp) cc_final: 0.8464 (mmt) REVERT: B 192 MET cc_start: 0.7845 (mmt) cc_final: 0.7482 (mmt) REVERT: B 227 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7817 (tm-30) REVERT: B 265 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8504 (mp10) REVERT: C 227 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8229 (tm-30) REVERT: C 230 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7447 (mm-30) REVERT: C 328 LYS cc_start: 0.9036 (tttt) cc_final: 0.8777 (mmtm) REVERT: D 49 MET cc_start: 0.4996 (mtt) cc_final: 0.4159 (mpp) REVERT: E 49 MET cc_start: 0.3267 (mtt) cc_final: 0.3043 (mpp) REVERT: E 265 GLN cc_start: 0.8737 (mp10) cc_final: 0.8491 (mp10) outliers start: 39 outliers final: 24 residues processed: 192 average time/residue: 0.1057 time to fit residues: 31.6906 Evaluate side-chains 165 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 227 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 83 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 41 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 26 optimal weight: 0.0030 overall best weight: 3.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN ** E 117 ASN ** 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 = 0.3146 r_free = 0.3146 target = 0.052204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046563 restraints weight = 82571.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047867 restraints weight = 43332.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048730 restraints weight = 26806.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049339 restraints weight = 18520.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049796 restraints weight = 13710.096| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14910 Z= 0.153 Angle : 0.675 10.760 20235 Z= 0.319 Chirality : 0.046 0.191 2250 Planarity : 0.004 0.036 2580 Dihedral : 9.389 125.729 2080 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.18 % Allowed : 10.26 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1845 helix: 0.04 (0.20), residues: 755 sheet: -0.63 (0.32), residues: 270 loop : -1.30 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 337 TYR 0.019 0.001 TYR D 225 PHE 0.011 0.001 PHE A 264 TRP 0.026 0.002 TRP C 358 HIS 0.006 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00339 (14910) covalent geometry : angle 0.67502 (20235) hydrogen bonds : bond 0.03463 ( 585) hydrogen bonds : angle 5.10220 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8413 (tm-30) REVERT: A 271 MET cc_start: 0.8532 (tpp) cc_final: 0.8203 (tpp) REVERT: B 83 ASP cc_start: 0.8280 (m-30) cc_final: 0.7958 (m-30) REVERT: B 192 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7563 (mmt) REVERT: B 227 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8060 (tm-30) REVERT: B 265 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8461 (mp10) REVERT: B 307 MET cc_start: 0.8285 (mtt) cc_final: 0.8014 (mtt) REVERT: C 227 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 230 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7487 (mm-30) REVERT: C 328 LYS cc_start: 0.9045 (tttt) cc_final: 0.8793 (mmtm) REVERT: D 49 MET cc_start: 0.4531 (mtt) cc_final: 0.3987 (mpp) REVERT: D 192 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7208 (mmt) REVERT: D 265 GLN cc_start: 0.8577 (mp10) cc_final: 0.8208 (mp10) REVERT: D 358 TRP cc_start: 0.8413 (m100) cc_final: 0.8186 (m100) REVERT: E 49 MET cc_start: 0.3251 (mtt) cc_final: 0.2982 (mpp) REVERT: E 192 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7454 (mmt) REVERT: E 265 GLN cc_start: 0.8731 (mp10) cc_final: 0.8511 (mp10) outliers start: 34 outliers final: 25 residues processed: 175 average time/residue: 0.0995 time to fit residues: 27.3698 Evaluate side-chains 168 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 200 TYR Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 28 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 122 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 58 optimal weight: 0.0670 chunk 80 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN ** E 117 ASN ** 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 = 0.3154 r_free = 0.3154 target = 0.052475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046806 restraints weight = 81333.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.048115 restraints weight = 43051.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049024 restraints weight = 26722.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049607 restraints weight = 18376.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.050057 restraints weight = 13689.163| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14910 Z= 0.129 Angle : 0.648 9.236 20235 Z= 0.305 Chirality : 0.046 0.199 2250 Planarity : 0.004 0.034 2580 Dihedral : 9.297 126.905 2080 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.31 % Allowed : 10.77 % Favored : 86.92 % 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: -0.78 (0.21), residues: 1845 helix: 0.25 (0.20), residues: 755 sheet: -0.47 (0.30), residues: 295 loop : -1.21 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 337 TYR 0.019 0.001 TYR D 225 PHE 0.012 0.001 PHE D 264 TRP 0.014 0.001 TRP C 358 HIS 0.006 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00289 (14910) covalent geometry : angle 0.64788 (20235) hydrogen bonds : bond 0.03293 ( 585) hydrogen bonds : angle 4.97328 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8395 (tm-30) REVERT: A 271 MET cc_start: 0.8493 (tpp) cc_final: 0.8169 (tpp) REVERT: A 327 MET cc_start: 0.8055 (mpp) cc_final: 0.6940 (ttt) REVERT: B 18 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7492 (mmm) REVERT: B 83 ASP cc_start: 0.8206 (m-30) cc_final: 0.7962 (m-30) REVERT: B 192 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7520 (mmt) REVERT: B 227 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 265 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8455 (mp10) REVERT: B 279 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9160 (m) REVERT: B 307 MET cc_start: 0.8211 (mtt) cc_final: 0.7906 (mtt) REVERT: C 227 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8344 (tm-30) REVERT: C 230 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7721 (mm-30) REVERT: C 265 GLN cc_start: 0.8697 (mp10) cc_final: 0.8463 (mp10) REVERT: C 307 MET cc_start: 0.7856 (mtt) cc_final: 0.7275 (mtt) REVERT: C 328 LYS cc_start: 0.8993 (tttt) cc_final: 0.8764 (mmtm) REVERT: D 49 MET cc_start: 0.4495 (mtt) cc_final: 0.3955 (mpp) REVERT: D 192 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7335 (mmt) REVERT: D 230 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7470 (mm-30) REVERT: D 265 GLN cc_start: 0.8584 (mp10) cc_final: 0.8141 (mp10) REVERT: D 358 TRP cc_start: 0.8362 (m100) cc_final: 0.8084 (m100) REVERT: E 49 MET cc_start: 0.3348 (mtt) cc_final: 0.3066 (mpp) REVERT: E 192 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7463 (mmt) REVERT: E 265 GLN cc_start: 0.8729 (mp10) cc_final: 0.8511 (mp10) outliers start: 36 outliers final: 23 residues processed: 176 average time/residue: 0.1011 time to fit residues: 28.1467 Evaluate side-chains 168 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 146 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 78 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 75 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.052527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046865 restraints weight = 81227.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.048170 restraints weight = 42971.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049035 restraints weight = 26738.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049647 restraints weight = 18543.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.050104 restraints weight = 13751.393| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14910 Z= 0.127 Angle : 0.646 10.212 20235 Z= 0.303 Chirality : 0.046 0.197 2250 Planarity : 0.004 0.034 2580 Dihedral : 9.256 127.781 2080 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.31 % Allowed : 11.03 % Favored : 86.67 % 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: -0.72 (0.21), residues: 1845 helix: 0.37 (0.20), residues: 755 sheet: -0.60 (0.29), residues: 325 loop : -1.18 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 337 TYR 0.019 0.001 TYR D 225 PHE 0.012 0.001 PHE D 264 TRP 0.023 0.002 TRP B 358 HIS 0.005 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00284 (14910) covalent geometry : angle 0.64571 (20235) hydrogen bonds : bond 0.03265 ( 585) hydrogen bonds : angle 4.88862 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.5044 (ppp) cc_final: 0.4624 (ppp) REVERT: A 123 GLN cc_start: 0.8802 (pt0) cc_final: 0.8504 (pt0) REVERT: A 227 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8427 (tm-30) REVERT: A 271 MET cc_start: 0.8546 (tpp) cc_final: 0.8182 (tpp) REVERT: A 279 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9043 (m) REVERT: A 307 MET cc_start: 0.8216 (mtt) cc_final: 0.7919 (mtt) REVERT: A 327 MET cc_start: 0.7901 (mpp) cc_final: 0.6829 (ttt) REVERT: B 18 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7529 (mmt) REVERT: B 83 ASP cc_start: 0.8175 (m-30) cc_final: 0.7946 (m-30) REVERT: B 192 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7555 (mmt) REVERT: B 227 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 265 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8443 (mp10) REVERT: B 279 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9130 (m) REVERT: B 307 MET cc_start: 0.8269 (mtt) cc_final: 0.7705 (mtt) REVERT: C 123 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8408 (tm-30) REVERT: C 227 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8300 (tm-30) REVERT: C 230 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 265 GLN cc_start: 0.8730 (mp10) cc_final: 0.8447 (mp10) REVERT: C 307 MET cc_start: 0.7957 (mtt) cc_final: 0.7267 (mtt) REVERT: C 327 MET cc_start: 0.6812 (tpp) cc_final: 0.6558 (tpt) REVERT: C 328 LYS cc_start: 0.8993 (tttt) cc_final: 0.8745 (mmtm) REVERT: D 49 MET cc_start: 0.4254 (mtt) cc_final: 0.3757 (mpp) REVERT: D 192 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7477 (mmt) REVERT: D 265 GLN cc_start: 0.8581 (mp10) cc_final: 0.8120 (mp10) REVERT: D 307 MET cc_start: 0.8248 (mtt) cc_final: 0.7979 (mtt) REVERT: D 358 TRP cc_start: 0.8359 (m100) cc_final: 0.8039 (m100) REVERT: E 49 MET cc_start: 0.3419 (mtt) cc_final: 0.3183 (mpp) REVERT: E 192 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7438 (mmt) REVERT: E 265 GLN cc_start: 0.8747 (mp10) cc_final: 0.8546 (mp10) outliers start: 36 outliers final: 22 residues processed: 176 average time/residue: 0.0969 time to fit residues: 27.4470 Evaluate side-chains 167 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 67 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN ** E 117 ASN ** 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 = 0.3129 r_free = 0.3129 target = 0.051594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045986 restraints weight = 81531.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047259 restraints weight = 43082.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048135 restraints weight = 26815.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048733 restraints weight = 18502.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049176 restraints weight = 13771.615| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14910 Z= 0.159 Angle : 0.669 10.256 20235 Z= 0.314 Chirality : 0.046 0.181 2250 Planarity : 0.004 0.033 2580 Dihedral : 9.311 129.994 2080 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.76 % Allowed : 10.83 % Favored : 86.41 % 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: -0.66 (0.21), residues: 1845 helix: 0.42 (0.20), residues: 755 sheet: -0.63 (0.29), residues: 335 loop : -1.13 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 337 TYR 0.023 0.001 TYR E 225 PHE 0.012 0.001 PHE B 264 TRP 0.014 0.001 TRP B 358 HIS 0.006 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00356 (14910) covalent geometry : angle 0.66885 (20235) hydrogen bonds : bond 0.03379 ( 585) hydrogen bonds : angle 4.91118 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.4970 (ppp) cc_final: 0.4539 (ppp) REVERT: A 123 GLN cc_start: 0.8802 (pt0) cc_final: 0.8530 (pt0) REVERT: A 227 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8395 (tm-30) REVERT: A 271 MET cc_start: 0.8565 (tpp) cc_final: 0.8188 (tpp) REVERT: A 279 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9013 (m) REVERT: A 327 MET cc_start: 0.7851 (mpp) cc_final: 0.6806 (tpt) REVERT: B 18 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7579 (mmm) REVERT: B 83 ASP cc_start: 0.8193 (m-30) cc_final: 0.7923 (m-30) REVERT: B 121 MET cc_start: 0.8656 (ttp) cc_final: 0.8334 (tmm) REVERT: B 192 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7571 (mmt) REVERT: B 227 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 265 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8437 (mp10) REVERT: B 307 MET cc_start: 0.8250 (mtt) cc_final: 0.7701 (mtt) REVERT: C 227 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8323 (tm-30) REVERT: C 265 GLN cc_start: 0.8687 (mp10) cc_final: 0.8382 (mp10) REVERT: C 307 MET cc_start: 0.8170 (mtt) cc_final: 0.7494 (mtt) REVERT: C 327 MET cc_start: 0.6929 (tpp) cc_final: 0.6701 (tpt) REVERT: D 49 MET cc_start: 0.4426 (mtt) cc_final: 0.3743 (mpp) REVERT: D 84 MET cc_start: 0.8952 (mmm) cc_final: 0.8714 (tpp) REVERT: D 192 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7459 (mmt) REVERT: D 265 GLN cc_start: 0.8587 (mp10) cc_final: 0.8127 (mp10) REVERT: D 307 MET cc_start: 0.8234 (mtt) cc_final: 0.7926 (mtt) REVERT: D 358 TRP cc_start: 0.8359 (m100) cc_final: 0.8069 (m100) REVERT: E 18 MET cc_start: 0.8048 (mmp) cc_final: 0.7739 (mmp) REVERT: E 49 MET cc_start: 0.3473 (mtt) cc_final: 0.3239 (mpp) REVERT: E 192 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7480 (mmt) outliers start: 43 outliers final: 23 residues processed: 176 average time/residue: 0.0964 time to fit residues: 27.1927 Evaluate side-chains 166 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** 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 = 0.3118 r_free = 0.3118 target = 0.051159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.045549 restraints weight = 81854.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.046838 restraints weight = 42801.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047714 restraints weight = 26504.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048318 restraints weight = 18287.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048737 restraints weight = 13536.610| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14910 Z= 0.170 Angle : 0.699 11.789 20235 Z= 0.327 Chirality : 0.047 0.191 2250 Planarity : 0.004 0.032 2580 Dihedral : 9.397 130.121 2080 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.37 % Allowed : 10.83 % Favored : 86.79 % 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: -0.71 (0.21), residues: 1845 helix: 0.39 (0.20), residues: 755 sheet: -0.69 (0.29), residues: 335 loop : -1.14 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 337 TYR 0.024 0.001 TYR E 225 PHE 0.012 0.001 PHE C 264 TRP 0.011 0.001 TRP B 358 HIS 0.005 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00381 (14910) covalent geometry : angle 0.69877 (20235) hydrogen bonds : bond 0.03445 ( 585) hydrogen bonds : angle 4.93877 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.5286 (ppp) cc_final: 0.4792 (ppp) REVERT: A 123 GLN cc_start: 0.8841 (pt0) cc_final: 0.8549 (pt0) REVERT: A 227 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8409 (tm-30) REVERT: A 271 MET cc_start: 0.8594 (tpp) cc_final: 0.8169 (tpp) REVERT: A 279 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9007 (m) REVERT: B 18 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7556 (mmm) REVERT: B 47 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8452 (t) REVERT: B 83 ASP cc_start: 0.8182 (m-30) cc_final: 0.7905 (m-30) REVERT: B 121 MET cc_start: 0.8601 (ttp) cc_final: 0.8349 (tmm) REVERT: B 192 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7580 (mmt) REVERT: B 227 GLN cc_start: 0.8491 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 228 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8116 (mm-30) REVERT: B 265 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8393 (mp10) REVERT: B 307 MET cc_start: 0.8353 (mtt) cc_final: 0.7964 (mtt) REVERT: C 227 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8297 (tm-30) REVERT: C 230 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7474 (mm-30) REVERT: C 265 GLN cc_start: 0.8656 (mp10) cc_final: 0.8452 (mp10) REVERT: C 307 MET cc_start: 0.8107 (mtt) cc_final: 0.7442 (mtt) REVERT: D 49 MET cc_start: 0.4517 (mtt) cc_final: 0.4295 (mtt) REVERT: D 84 MET cc_start: 0.9027 (mmm) cc_final: 0.8794 (tpp) REVERT: D 192 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7509 (mmt) REVERT: D 265 GLN cc_start: 0.8558 (mp10) cc_final: 0.8131 (mp10) REVERT: D 307 MET cc_start: 0.8303 (mtt) cc_final: 0.7930 (mtt) REVERT: D 358 TRP cc_start: 0.8364 (m100) cc_final: 0.8073 (m100) REVERT: E 49 MET cc_start: 0.3718 (mtt) cc_final: 0.3422 (mpp) REVERT: E 192 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7474 (mmt) outliers start: 37 outliers final: 27 residues processed: 168 average time/residue: 0.0973 time to fit residues: 25.9376 Evaluate side-chains 173 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 227 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 137 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** D 227 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 = 0.3116 r_free = 0.3116 target = 0.051052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045464 restraints weight = 82703.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046742 restraints weight = 43531.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047611 restraints weight = 27008.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048214 restraints weight = 18651.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048655 restraints weight = 13806.758| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14910 Z= 0.166 Angle : 0.699 14.024 20235 Z= 0.328 Chirality : 0.047 0.187 2250 Planarity : 0.004 0.032 2580 Dihedral : 9.391 130.026 2080 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.24 % Allowed : 10.77 % Favored : 86.99 % 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: -0.70 (0.21), residues: 1845 helix: 0.38 (0.20), residues: 755 sheet: -0.69 (0.28), residues: 335 loop : -1.12 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 337 TYR 0.021 0.001 TYR D 225 PHE 0.013 0.001 PHE C 264 TRP 0.010 0.001 TRP B 358 HIS 0.006 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00372 (14910) covalent geometry : angle 0.69920 (20235) hydrogen bonds : bond 0.03452 ( 585) hydrogen bonds : angle 4.91217 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8800 (pt0) cc_final: 0.8524 (pt0) REVERT: A 227 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8422 (tm-30) REVERT: A 271 MET cc_start: 0.8520 (tpp) cc_final: 0.8089 (tpp) REVERT: A 279 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.8978 (m) REVERT: B 18 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7559 (mmm) REVERT: B 83 ASP cc_start: 0.8197 (m-30) cc_final: 0.7975 (m-30) REVERT: B 121 MET cc_start: 0.8578 (ttp) cc_final: 0.8345 (tmm) REVERT: B 192 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7560 (mmt) REVERT: B 227 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 228 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8125 (mm-30) REVERT: B 265 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8364 (mp10) REVERT: B 307 MET cc_start: 0.8380 (mtt) cc_final: 0.7977 (mtt) REVERT: C 18 MET cc_start: 0.8148 (mmt) cc_final: 0.7931 (mmt) REVERT: C 227 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8294 (tm-30) REVERT: C 230 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7489 (mm-30) REVERT: C 307 MET cc_start: 0.8130 (mtt) cc_final: 0.7458 (mtt) REVERT: C 315 MET cc_start: 0.8993 (mmm) cc_final: 0.8637 (mmm) REVERT: D 49 MET cc_start: 0.4498 (mtt) cc_final: 0.3881 (mpp) REVERT: D 84 MET cc_start: 0.9049 (mmm) cc_final: 0.8823 (mmm) REVERT: D 192 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7519 (mmt) REVERT: D 265 GLN cc_start: 0.8521 (mp10) cc_final: 0.8133 (mp10) REVERT: D 307 MET cc_start: 0.8343 (mtt) cc_final: 0.7925 (mtt) REVERT: D 358 TRP cc_start: 0.8333 (m100) cc_final: 0.8012 (m100) REVERT: E 18 MET cc_start: 0.8058 (mmp) cc_final: 0.7702 (mmp) REVERT: E 49 MET cc_start: 0.3781 (mtt) cc_final: 0.3513 (mpp) REVERT: E 192 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7499 (mmt) outliers start: 35 outliers final: 27 residues processed: 170 average time/residue: 0.0986 time to fit residues: 26.6667 Evaluate side-chains 172 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 227 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 22 optimal weight: 0.0670 chunk 80 optimal weight: 0.0370 chunk 5 optimal weight: 0.0370 chunk 171 optimal weight: 20.0000 chunk 137 optimal weight: 0.1980 chunk 156 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.0676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 117 ASN D 139 GLN E 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047527 restraints weight = 80488.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048836 restraints weight = 42120.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049739 restraints weight = 25940.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050334 restraints weight = 17667.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.050778 restraints weight = 13042.067| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14910 Z= 0.105 Angle : 0.672 14.449 20235 Z= 0.311 Chirality : 0.046 0.155 2250 Planarity : 0.004 0.034 2580 Dihedral : 9.121 125.583 2080 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.60 % Allowed : 11.73 % Favored : 86.67 % 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: -0.43 (0.21), residues: 1845 helix: 0.43 (0.20), residues: 755 sheet: -0.12 (0.31), residues: 295 loop : -0.97 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 337 TYR 0.013 0.001 TYR D 225 PHE 0.010 0.001 PHE C 264 TRP 0.012 0.002 TRP C 358 HIS 0.004 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00231 (14910) covalent geometry : angle 0.67154 (20235) hydrogen bonds : bond 0.03276 ( 585) hydrogen bonds : angle 4.70140 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8891 (pt0) cc_final: 0.8689 (pt0) REVERT: A 227 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8449 (tm-30) REVERT: A 230 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7714 (mm-30) REVERT: A 279 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9008 (m) REVERT: B 18 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7379 (mmt) REVERT: B 83 ASP cc_start: 0.8103 (m-30) cc_final: 0.7849 (m-30) REVERT: B 192 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7384 (mmt) REVERT: B 227 GLN cc_start: 0.8543 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 228 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8154 (mm-30) REVERT: B 280 THR cc_start: 0.9350 (m) cc_final: 0.9148 (p) REVERT: B 307 MET cc_start: 0.8420 (mtt) cc_final: 0.8019 (mtt) REVERT: C 18 MET cc_start: 0.8030 (mmt) cc_final: 0.7821 (mmp) REVERT: C 227 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8296 (tm-30) REVERT: C 307 MET cc_start: 0.8107 (mtt) cc_final: 0.7458 (mtt) REVERT: C 315 MET cc_start: 0.8965 (mmm) cc_final: 0.8665 (mmm) REVERT: D 49 MET cc_start: 0.4397 (mtt) cc_final: 0.3896 (mpp) REVERT: D 84 MET cc_start: 0.8996 (mmm) cc_final: 0.8768 (mmm) REVERT: D 265 GLN cc_start: 0.8451 (mp10) cc_final: 0.8071 (mp10) REVERT: D 307 MET cc_start: 0.8203 (mtt) cc_final: 0.7738 (mtt) REVERT: D 358 TRP cc_start: 0.8344 (m100) cc_final: 0.8047 (m100) REVERT: E 49 MET cc_start: 0.3688 (mtt) cc_final: 0.3382 (mpp) REVERT: E 358 TRP cc_start: 0.8411 (m100) cc_final: 0.7994 (m100) outliers start: 25 outliers final: 17 residues processed: 175 average time/residue: 0.1028 time to fit residues: 28.2126 Evaluate side-chains 162 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 89 HIS Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 227 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 24 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 172 optimal weight: 0.2980 chunk 10 optimal weight: 0.0170 chunk 21 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 overall best weight: 2.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.052565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.046946 restraints weight = 81443.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048264 restraints weight = 42905.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.049157 restraints weight = 26530.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049756 restraints weight = 18209.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050167 restraints weight = 13482.103| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14910 Z= 0.124 Angle : 0.687 14.547 20235 Z= 0.318 Chirality : 0.046 0.164 2250 Planarity : 0.003 0.033 2580 Dihedral : 9.079 127.214 2080 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.60 % Allowed : 12.24 % Favored : 86.15 % 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: -0.41 (0.21), residues: 1845 helix: 0.45 (0.20), residues: 755 sheet: -0.15 (0.30), residues: 305 loop : -0.95 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 337 TYR 0.015 0.001 TYR D 225 PHE 0.009 0.001 PHE A 264 TRP 0.012 0.001 TRP B 358 HIS 0.004 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00281 (14910) covalent geometry : angle 0.68738 (20235) hydrogen bonds : bond 0.03278 ( 585) hydrogen bonds : angle 4.69710 ( 1575) =============================================================================== Job complete usr+sys time: 1734.96 seconds wall clock time: 31 minutes 2.88 seconds (1862.88 seconds total)