Starting phenix.real_space_refine on Thu Jun 12 23:44:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iug_9734/06_2025/6iug_9734.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iug_9734/06_2025/6iug_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6iug_9734/06_2025/6iug_9734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iug_9734/06_2025/6iug_9734.map" model { file = "/net/cci-nas-00/data/ceres_data/6iug_9734/06_2025/6iug_9734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iug_9734/06_2025/6iug_9734.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D Time building chain proxies: 6.60, per 1000 atoms: 0.45 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: 3.31 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.85 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: 4.61 Time building geometry restraints manager: 4.06 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 32.930 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.610 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.003 TRP A 342 HIS 0.013 0.002 HIS B 89 PHE 0.017 0.002 PHE E 264 TYR 0.028 0.002 TYR D 296 ARG 0.008 0.001 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.20530 ( 585) hydrogen bonds : angle 7.60298 ( 1575) covalent geometry : bond 0.00508 (14910) covalent geometry : angle 0.90096 (20235) *********************** 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 : 1.558 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: 0.8392 (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: 0.8557 (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: 0.9336 (mm-40) cc_final: 0.9018 (mm-40) outliers start: 15 outliers final: 5 residues processed: 284 average time/residue: 0.2858 time to fit residues: 114.7821 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 : 1.730 ------------------------------------------------------------------------------- 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 156 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 88 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 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 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 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047663 restraints weight = 80963.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048969 restraints weight = 42756.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049833 restraints weight = 26538.863| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14910 Z= 0.146 Angle : 0.687 7.810 20235 Z= 0.337 Chirality : 0.046 0.175 2250 Planarity : 0.005 0.049 2580 Dihedral : 10.143 116.846 2089 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.63 % Allowed : 6.79 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.19), residues: 1845 helix: -0.87 (0.18), residues: 750 sheet: -1.48 (0.30), residues: 300 loop : -1.78 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 358 HIS 0.006 0.001 HIS C 277 PHE 0.008 0.001 PHE D 264 TYR 0.028 0.002 TYR E 225 ARG 0.005 0.001 ARG B 337 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 585) hydrogen bonds : angle 5.55359 ( 1575) covalent geometry : bond 0.00324 (14910) covalent geometry : angle 0.68748 (20235) *********************** 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: 41 poor density : 186 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8456 (tm-30) REVERT: B 83 ASP cc_start: 0.8377 (m-30) cc_final: 0.8130 (m-30) REVERT: B 121 MET cc_start: 0.8811 (ttp) cc_final: 0.8428 (tmm) REVERT: B 125 MET cc_start: 0.8913 (mmp) cc_final: 0.8579 (mmt) REVERT: B 192 MET cc_start: 0.7897 (mmt) cc_final: 0.7631 (mmt) REVERT: B 265 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8532 (mp10) REVERT: C 230 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7582 (mm-30) REVERT: D 230 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7588 (mm-30) REVERT: E 83 ASP cc_start: 0.8379 (m-30) cc_final: 0.8149 (m-30) REVERT: E 224 ASP cc_start: 0.7947 (t0) cc_final: 0.7424 (t70) REVERT: E 230 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7558 (mm-30) outliers start: 41 outliers final: 27 residues processed: 219 average time/residue: 0.2480 time to fit residues: 82.4108 Evaluate side-chains 175 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 166 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 chunk 164 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 147 optimal weight: 30.0000 chunk 95 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 139 GLN A 248 GLN C 117 ASN D 298 ASN E 356 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.051982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046353 restraints weight = 81980.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047660 restraints weight = 43315.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048530 restraints weight = 26870.098| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14910 Z= 0.167 Angle : 0.699 9.606 20235 Z= 0.334 Chirality : 0.047 0.164 2250 Planarity : 0.004 0.039 2580 Dihedral : 9.902 124.529 2085 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.69 % Allowed : 8.91 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.20), residues: 1845 helix: -0.27 (0.19), residues: 755 sheet: -0.88 (0.32), residues: 270 loop : -1.53 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 358 HIS 0.006 0.001 HIS C 277 PHE 0.012 0.001 PHE D 264 TYR 0.019 0.002 TYR D 225 ARG 0.003 0.000 ARG B 337 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 585) hydrogen bonds : angle 5.29174 ( 1575) covalent geometry : bond 0.00369 (14910) covalent geometry : angle 0.69942 (20235) *********************** 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 196 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8812 (ttp) cc_final: 0.8582 (tmm) REVERT: A 227 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8461 (tm-30) REVERT: B 83 ASP cc_start: 0.8377 (m-30) cc_final: 0.8063 (m-30) REVERT: B 121 MET cc_start: 0.8771 (ttp) cc_final: 0.8392 (tmm) REVERT: B 125 MET cc_start: 0.8870 (mmp) cc_final: 0.8530 (mmt) REVERT: B 192 MET cc_start: 0.7865 (mmt) cc_final: 0.7486 (mmt) REVERT: C 227 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 230 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7539 (mm-30) REVERT: D 358 TRP cc_start: 0.8440 (m100) cc_final: 0.8163 (m100) REVERT: E 49 MET cc_start: 0.3455 (mtt) cc_final: 0.3189 (mpp) REVERT: E 230 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7580 (mm-30) outliers start: 42 outliers final: 26 residues processed: 185 average time/residue: 0.2424 time to fit residues: 69.4107 Evaluate side-chains 163 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 69 LEU 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 49 MET 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 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 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 227 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 97 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 28 optimal weight: 0.0980 chunk 2 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 356 GLN C 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045919 restraints weight = 81637.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.047215 restraints weight = 43032.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048085 restraints weight = 26586.976| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14910 Z= 0.164 Angle : 0.690 10.613 20235 Z= 0.327 Chirality : 0.046 0.201 2250 Planarity : 0.004 0.035 2580 Dihedral : 9.580 126.531 2080 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.05 % Allowed : 11.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.20), residues: 1845 helix: 0.03 (0.20), residues: 755 sheet: -1.05 (0.30), residues: 300 loop : -1.38 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 358 HIS 0.007 0.001 HIS C 277 PHE 0.012 0.001 PHE A 264 TYR 0.021 0.001 TYR D 225 ARG 0.002 0.000 ARG D 337 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 585) hydrogen bonds : angle 5.12116 ( 1575) covalent geometry : bond 0.00367 (14910) covalent geometry : angle 0.69044 (20235) *********************** 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 175 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.5063 (ppp) cc_final: 0.4473 (ppp) REVERT: A 121 MET cc_start: 0.8796 (ttp) cc_final: 0.8593 (tmm) REVERT: A 227 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8482 (tm-30) REVERT: A 271 MET cc_start: 0.8579 (tpp) cc_final: 0.8267 (tpp) REVERT: B 83 ASP cc_start: 0.8373 (m-30) cc_final: 0.8020 (m-30) REVERT: B 121 MET cc_start: 0.8752 (ttp) cc_final: 0.8384 (tmm) REVERT: B 125 MET cc_start: 0.8833 (mmp) cc_final: 0.8577 (mmt) REVERT: B 192 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7543 (mmt) REVERT: B 265 GLN cc_start: 0.8544 (mp10) cc_final: 0.8273 (mp10) REVERT: C 227 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8437 (tm-30) REVERT: C 230 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7764 (mm-30) REVERT: D 49 MET cc_start: 0.6044 (mmm) cc_final: 0.5653 (mpp) REVERT: D 192 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7289 (mmt) REVERT: D 265 GLN cc_start: 0.8651 (mp10) cc_final: 0.8336 (mp10) REVERT: D 358 TRP cc_start: 0.8415 (m100) cc_final: 0.8131 (m100) REVERT: E 49 MET cc_start: 0.3337 (mtt) cc_final: 0.3079 (mpp) REVERT: E 192 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7479 (mmt) REVERT: E 230 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7658 (mm-30) outliers start: 32 outliers final: 22 residues processed: 168 average time/residue: 0.2469 time to fit residues: 64.1697 Evaluate side-chains 158 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 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 D residue 200 TYR 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 37 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045808 restraints weight = 82884.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.047090 restraints weight = 43667.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047981 restraints weight = 27099.752| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3595 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= 0.152 Angle : 0.670 9.528 20235 Z= 0.316 Chirality : 0.046 0.168 2250 Planarity : 0.004 0.033 2580 Dihedral : 9.483 128.172 2080 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1845 helix: 0.23 (0.20), residues: 755 sheet: -0.87 (0.30), residues: 300 loop : -1.26 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 358 HIS 0.006 0.001 HIS C 277 PHE 0.013 0.001 PHE D 264 TYR 0.021 0.001 TYR D 225 ARG 0.003 0.000 ARG B 337 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 585) hydrogen bonds : angle 5.01567 ( 1575) covalent geometry : bond 0.00339 (14910) covalent geometry : angle 0.67050 (20235) *********************** 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 178 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8049 (mmm) cc_final: 0.7806 (mmt) REVERT: A 46 MET cc_start: 0.5269 (ppp) cc_final: 0.4726 (ppp) REVERT: A 227 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8479 (tm-30) REVERT: A 271 MET cc_start: 0.8594 (tpp) cc_final: 0.8292 (tpp) REVERT: A 327 MET cc_start: 0.8012 (mpp) cc_final: 0.6915 (ttt) REVERT: B 18 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7555 (mmm) REVERT: B 83 ASP cc_start: 0.8333 (m-30) cc_final: 0.8070 (m-30) REVERT: B 121 MET cc_start: 0.8742 (ttp) cc_final: 0.8368 (tmm) REVERT: B 125 MET cc_start: 0.8849 (mmp) cc_final: 0.8620 (mmt) REVERT: B 192 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7562 (mmt) REVERT: B 227 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 279 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9133 (m) REVERT: C 227 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8372 (tm-30) REVERT: C 230 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7952 (mm-30) REVERT: C 336 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: D 49 MET cc_start: 0.6344 (mmm) cc_final: 0.5291 (mpp) REVERT: D 192 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7399 (mmt) REVERT: D 358 TRP cc_start: 0.8431 (m100) cc_final: 0.8099 (m100) REVERT: E 49 MET cc_start: 0.3359 (mtt) cc_final: 0.3100 (mpp) REVERT: E 192 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7470 (mmt) REVERT: E 230 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7701 (mm-30) outliers start: 37 outliers final: 19 residues processed: 173 average time/residue: 0.2276 time to fit residues: 61.7715 Evaluate side-chains 159 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 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 89 HIS Chi-restraints excluded: chain C residue 117 ASN 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 C residue 336 GLU 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 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 100 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 117 ASN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.043774 restraints weight = 84556.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.045050 restraints weight = 44113.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045906 restraints weight = 27344.761| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14910 Z= 0.246 Angle : 0.762 10.354 20235 Z= 0.364 Chirality : 0.049 0.240 2250 Planarity : 0.004 0.034 2580 Dihedral : 9.784 129.895 2080 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.50 % Allowed : 11.22 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1845 helix: 0.12 (0.19), residues: 755 sheet: -0.97 (0.28), residues: 335 loop : -1.47 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 358 HIS 0.008 0.002 HIS C 277 PHE 0.015 0.002 PHE B 264 TYR 0.027 0.002 TYR D 225 ARG 0.003 0.000 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 585) hydrogen bonds : angle 5.23956 ( 1575) covalent geometry : bond 0.00545 (14910) covalent geometry : angle 0.76194 (20235) *********************** 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 171 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8086 (mmm) cc_final: 0.7842 (mmt) REVERT: A 46 MET cc_start: 0.5833 (ppp) cc_final: 0.5596 (ppp) REVERT: A 227 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8508 (tm-30) REVERT: A 271 MET cc_start: 0.8656 (tpp) cc_final: 0.8333 (tpp) REVERT: A 279 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.9013 (m) REVERT: B 18 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7694 (mmm) REVERT: B 83 ASP cc_start: 0.8318 (m-30) cc_final: 0.8033 (m-30) REVERT: B 121 MET cc_start: 0.8751 (ttp) cc_final: 0.8402 (tmm) REVERT: B 125 MET cc_start: 0.8864 (mmp) cc_final: 0.8587 (mmt) REVERT: B 192 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7679 (mmt) REVERT: B 227 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8066 (tm-30) REVERT: B 279 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9122 (m) REVERT: C 227 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8388 (tm-30) REVERT: C 307 MET cc_start: 0.8059 (mtt) cc_final: 0.7544 (mtt) REVERT: D 49 MET cc_start: 0.6418 (mmm) cc_final: 0.5684 (mpp) REVERT: D 84 MET cc_start: 0.9079 (mmm) cc_final: 0.8806 (mmm) REVERT: D 120 LYS cc_start: 0.9048 (mttt) cc_final: 0.8840 (mttp) REVERT: D 192 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7454 (mmt) REVERT: D 358 TRP cc_start: 0.8445 (m100) cc_final: 0.8122 (m100) REVERT: E 49 MET cc_start: 0.3851 (mtt) cc_final: 0.3646 (mtt) REVERT: E 192 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7549 (mmt) REVERT: E 230 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7975 (mm-30) outliers start: 39 outliers final: 23 residues processed: 164 average time/residue: 0.2423 time to fit residues: 61.5095 Evaluate side-chains 160 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 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 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 78 VAL Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 290 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 115 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3062 r_free = 0.3062 target = 0.049186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.043563 restraints weight = 84654.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.044837 restraints weight = 44004.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.045717 restraints weight = 27297.565| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14910 Z= 0.228 Angle : 0.742 10.045 20235 Z= 0.353 Chirality : 0.048 0.239 2250 Planarity : 0.004 0.034 2580 Dihedral : 9.836 130.185 2080 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 2.56 % Allowed : 11.09 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1845 helix: 0.12 (0.19), residues: 755 sheet: -1.16 (0.26), residues: 365 loop : -1.50 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 358 HIS 0.008 0.002 HIS C 277 PHE 0.014 0.001 PHE A 264 TYR 0.027 0.002 TYR D 225 ARG 0.005 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 585) hydrogen bonds : angle 5.17870 ( 1575) covalent geometry : bond 0.00506 (14910) covalent geometry : angle 0.74199 (20235) *********************** 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 176 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 271 MET cc_start: 0.8657 (tpp) cc_final: 0.8272 (tpp) REVERT: A 279 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8963 (m) REVERT: B 18 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7626 (mmm) REVERT: B 83 ASP cc_start: 0.8350 (m-30) cc_final: 0.8037 (m-30) REVERT: B 121 MET cc_start: 0.8731 (ttp) cc_final: 0.8395 (tmm) REVERT: B 192 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7659 (mmt) REVERT: C 18 MET cc_start: 0.8167 (mmt) cc_final: 0.7924 (mmp) REVERT: C 227 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8394 (tm-30) REVERT: C 307 MET cc_start: 0.8141 (mtt) cc_final: 0.7667 (mtt) REVERT: D 49 MET cc_start: 0.6563 (mmm) cc_final: 0.5799 (mpp) REVERT: D 84 MET cc_start: 0.9120 (mmm) cc_final: 0.8881 (mmm) REVERT: D 120 LYS cc_start: 0.9013 (mttt) cc_final: 0.8745 (mtmm) REVERT: D 192 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7467 (mmt) REVERT: D 358 TRP cc_start: 0.8417 (m100) cc_final: 0.8069 (m100) REVERT: E 18 MET cc_start: 0.8129 (mmt) cc_final: 0.7869 (mmp) REVERT: E 49 MET cc_start: 0.3988 (mtt) cc_final: 0.3744 (mpp) REVERT: E 192 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7562 (mmt) REVERT: E 230 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8053 (mm-30) outliers start: 40 outliers final: 22 residues processed: 168 average time/residue: 0.2368 time to fit residues: 61.2633 Evaluate side-chains 158 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 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 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 D residue 290 ASP 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: 0.6980 chunk 155 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 183 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3091 r_free = 0.3091 target = 0.050093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.044570 restraints weight = 82873.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045842 restraints weight = 43682.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.046691 restraints weight = 27100.887| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14910 Z= 0.155 Angle : 0.700 10.233 20235 Z= 0.330 Chirality : 0.047 0.223 2250 Planarity : 0.004 0.033 2580 Dihedral : 9.733 133.040 2080 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 1.99 % Allowed : 11.73 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1845 helix: 0.27 (0.20), residues: 755 sheet: -0.81 (0.29), residues: 300 loop : -1.24 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 358 HIS 0.007 0.001 HIS C 277 PHE 0.014 0.001 PHE D 264 TYR 0.026 0.001 TYR D 225 ARG 0.003 0.000 ARG C 337 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 585) hydrogen bonds : angle 5.01267 ( 1575) covalent geometry : bond 0.00349 (14910) covalent geometry : angle 0.70019 (20235) *********************** 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 170 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8599 (tm-30) REVERT: A 271 MET cc_start: 0.8597 (tpp) cc_final: 0.8188 (tpp) REVERT: A 279 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8983 (m) REVERT: B 18 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7370 (mmm) REVERT: B 83 ASP cc_start: 0.8286 (m-30) cc_final: 0.8039 (m-30) REVERT: B 121 MET cc_start: 0.8717 (ttp) cc_final: 0.8392 (tmm) REVERT: B 192 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7594 (mmt) REVERT: C 18 MET cc_start: 0.8086 (mmt) cc_final: 0.7828 (mmp) REVERT: C 227 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 265 GLN cc_start: 0.8707 (mp10) cc_final: 0.8428 (mp10) REVERT: C 307 MET cc_start: 0.8133 (mtt) cc_final: 0.7679 (mtt) REVERT: D 49 MET cc_start: 0.6615 (mmm) cc_final: 0.5553 (mpp) REVERT: D 84 MET cc_start: 0.9099 (mmm) cc_final: 0.8868 (mmm) REVERT: D 120 LYS cc_start: 0.9027 (mttt) cc_final: 0.8744 (mtmm) REVERT: D 192 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7499 (mmt) REVERT: D 358 TRP cc_start: 0.8410 (m100) cc_final: 0.8097 (m100) REVERT: E 230 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8080 (mm-30) outliers start: 31 outliers final: 21 residues processed: 163 average time/residue: 0.2331 time to fit residues: 59.0035 Evaluate side-chains 159 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 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 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 D residue 290 ASP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 112 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** 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 = 0.3064 r_free = 0.3064 target = 0.049401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.043848 restraints weight = 83852.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.045114 restraints weight = 43359.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045979 restraints weight = 26621.816| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14910 Z= 0.215 Angle : 0.750 10.715 20235 Z= 0.356 Chirality : 0.049 0.223 2250 Planarity : 0.004 0.034 2580 Dihedral : 9.805 134.472 2080 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 2.12 % Allowed : 12.24 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1845 helix: 0.14 (0.19), residues: 755 sheet: -1.07 (0.27), residues: 355 loop : -1.42 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 358 HIS 0.008 0.001 HIS C 277 PHE 0.016 0.001 PHE D 264 TYR 0.037 0.002 TYR D 225 ARG 0.003 0.000 ARG C 337 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 585) hydrogen bonds : angle 5.13536 ( 1575) covalent geometry : bond 0.00481 (14910) covalent geometry : angle 0.75011 (20235) *********************** 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 165 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 271 MET cc_start: 0.8594 (tpp) cc_final: 0.8207 (tpp) REVERT: A 279 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8968 (m) REVERT: B 18 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7522 (mmm) REVERT: B 83 ASP cc_start: 0.8272 (m-30) cc_final: 0.8037 (m-30) REVERT: B 121 MET cc_start: 0.8672 (ttp) cc_final: 0.8382 (tmm) REVERT: B 192 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7584 (mmt) REVERT: B 227 GLN cc_start: 0.8628 (tm130) cc_final: 0.8018 (tm-30) REVERT: C 18 MET cc_start: 0.8118 (mmt) cc_final: 0.7870 (mmp) REVERT: C 227 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8378 (tm-30) REVERT: C 265 GLN cc_start: 0.8699 (mp10) cc_final: 0.8371 (mp10) REVERT: C 307 MET cc_start: 0.8161 (mtt) cc_final: 0.7778 (mtt) REVERT: D 49 MET cc_start: 0.6715 (mmm) cc_final: 0.5923 (mpp) REVERT: D 84 MET cc_start: 0.9121 (mmm) cc_final: 0.8892 (mmm) REVERT: D 120 LYS cc_start: 0.9006 (mttt) cc_final: 0.8744 (mtmm) REVERT: D 192 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7448 (mmt) REVERT: D 358 TRP cc_start: 0.8410 (m100) cc_final: 0.8059 (m100) REVERT: E 49 MET cc_start: 0.4057 (mpp) cc_final: 0.3527 (mpp) REVERT: E 230 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8140 (mm-30) outliers start: 33 outliers final: 22 residues processed: 159 average time/residue: 0.2346 time to fit residues: 58.7928 Evaluate side-chains 157 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 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 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 C residue 336 GLU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 290 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 36 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046408 restraints weight = 81515.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047696 restraints weight = 42497.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.048562 restraints weight = 26099.692| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4424 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= 0.116 Angle : 0.688 12.591 20235 Z= 0.321 Chirality : 0.046 0.170 2250 Planarity : 0.004 0.037 2580 Dihedral : 9.539 132.075 2080 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.35 % Allowed : 12.88 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1845 helix: 0.33 (0.20), residues: 755 sheet: -0.56 (0.28), residues: 330 loop : -1.12 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 358 HIS 0.004 0.001 HIS C 277 PHE 0.010 0.001 PHE B 264 TYR 0.025 0.001 TYR E 225 ARG 0.003 0.000 ARG D 337 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 585) hydrogen bonds : angle 4.91921 ( 1575) covalent geometry : bond 0.00258 (14910) covalent geometry : angle 0.68806 (20235) ********************** 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 174 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8914 (pt0) cc_final: 0.8688 (pt0) REVERT: A 227 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8607 (tm-30) REVERT: A 279 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8968 (m) REVERT: B 18 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7112 (mmm) REVERT: B 83 ASP cc_start: 0.8150 (m-30) cc_final: 0.7907 (m-30) REVERT: B 121 MET cc_start: 0.8694 (ttp) cc_final: 0.8450 (tmm) REVERT: B 192 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7476 (mmt) REVERT: B 227 GLN cc_start: 0.8432 (tm130) cc_final: 0.7861 (tm-30) REVERT: C 18 MET cc_start: 0.7952 (mmt) cc_final: 0.7737 (mmp) REVERT: C 227 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8356 (tm-30) REVERT: C 265 GLN cc_start: 0.8741 (mp10) cc_final: 0.8417 (mp10) REVERT: C 307 MET cc_start: 0.8157 (mtt) cc_final: 0.7770 (mtt) REVERT: D 49 MET cc_start: 0.6704 (mmm) cc_final: 0.5587 (mpp) REVERT: D 84 MET cc_start: 0.9060 (mmm) cc_final: 0.8836 (mmm) REVERT: D 277 HIS cc_start: 0.8570 (p-80) cc_final: 0.8299 (p-80) REVERT: D 358 TRP cc_start: 0.8362 (m100) cc_final: 0.8067 (m100) REVERT: E 18 MET cc_start: 0.8338 (mmm) cc_final: 0.8022 (mmm) REVERT: E 49 MET cc_start: 0.4055 (mpp) cc_final: 0.3755 (mpp) REVERT: E 230 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8105 (mm-30) REVERT: E 358 TRP cc_start: 0.8446 (m100) cc_final: 0.8001 (m100) outliers start: 21 outliers final: 15 residues processed: 170 average time/residue: 0.2293 time to fit residues: 60.7073 Evaluate side-chains 165 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 HIS 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 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 89 HIS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 62 optimal weight: 0.0050 chunk 118 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 overall best weight: 2.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 ASN ** 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 = 0.3128 r_free = 0.3128 target = 0.051504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045994 restraints weight = 82777.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.047274 restraints weight = 43215.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.048156 restraints weight = 26609.193| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14910 Z= 0.137 Angle : 0.715 12.798 20235 Z= 0.334 Chirality : 0.047 0.177 2250 Planarity : 0.004 0.036 2580 Dihedral : 9.472 131.468 2080 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.35 % Allowed : 13.21 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.21), residues: 1845 helix: 0.33 (0.20), residues: 755 sheet: -0.72 (0.27), residues: 365 loop : -1.06 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 358 HIS 0.005 0.001 HIS E 277 PHE 0.011 0.001 PHE C 264 TYR 0.024 0.001 TYR D 225 ARG 0.003 0.000 ARG C 337 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 585) hydrogen bonds : angle 4.93972 ( 1575) covalent geometry : bond 0.00313 (14910) covalent geometry : angle 0.71463 (20235) =============================================================================== Job complete usr+sys time: 3739.75 seconds wall clock time: 67 minutes 4.41 seconds (4024.41 seconds total)