Starting phenix.real_space_refine on Sat Aug 23 10:13:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7f_38098/08_2025/8x7f_38098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7f_38098/08_2025/8x7f_38098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x7f_38098/08_2025/8x7f_38098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7f_38098/08_2025/8x7f_38098.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x7f_38098/08_2025/8x7f_38098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7f_38098/08_2025/8x7f_38098.map" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 48 5.16 5 C 7392 2.51 5 N 1932 2.21 5 O 2212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11596 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2850 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 333} Chain: "D" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2850 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 333} Chain: "G" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2850 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 333} Chain: "J" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2850 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 333} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAD': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAD': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAD': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAD': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.52, per 1000 atoms: 0.22 Number of scatterers: 11596 At special positions: 0 Unit cell: (82.07, 94.522, 99.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 12 15.00 O 2212 8.00 N 1932 7.00 C 7392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 476.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 55.1% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.815A pdb=" N SER A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 119 through 131 removed outlier: 3.639A pdb=" N PHE A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 262 through 273 removed outlier: 4.093A pdb=" N ASP A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 283 through 301 removed outlier: 3.826A pdb=" N ALA A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 324 removed outlier: 3.983A pdb=" N THR A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 361 through 379 removed outlier: 3.568A pdb=" N ARG A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 407 Processing helix chain 'D' and resid 77 through 89 removed outlier: 3.803A pdb=" N SER D 89 " --> pdb=" O GLN D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 119 through 131 removed outlier: 3.619A pdb=" N PHE D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 181 through 191 removed outlier: 4.101A pdb=" N GLN D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.526A pdb=" N ILE D 222 " --> pdb=" O TRP D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'D' and resid 243 through 255 Processing helix chain 'D' and resid 262 through 273 removed outlier: 4.107A pdb=" N ASP D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY D 273 " --> pdb=" O PHE D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 283 through 301 removed outlier: 3.740A pdb=" N ALA D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D 297 " --> pdb=" O GLN D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 324 removed outlier: 3.952A pdb=" N THR D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 Processing helix chain 'D' and resid 361 through 379 removed outlier: 3.627A pdb=" N ARG D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 407 Processing helix chain 'G' and resid 77 through 89 Processing helix chain 'G' and resid 101 through 112 Processing helix chain 'G' and resid 119 through 131 removed outlier: 3.609A pdb=" N PHE G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 169 Processing helix chain 'G' and resid 181 through 191 removed outlier: 4.163A pdb=" N GLN G 185 " --> pdb=" O ALA G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 214 Processing helix chain 'G' and resid 218 through 222 Processing helix chain 'G' and resid 226 through 230 Processing helix chain 'G' and resid 243 through 255 Processing helix chain 'G' and resid 262 through 273 removed outlier: 4.080A pdb=" N ASP G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 301 removed outlier: 4.359A pdb=" N LYS G 286 " --> pdb=" O SER G 282 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE G 287 " --> pdb=" O ASP G 283 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G 297 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 324 removed outlier: 3.975A pdb=" N THR G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 337 Processing helix chain 'G' and resid 361 through 379 removed outlier: 3.647A pdb=" N ARG G 365 " --> pdb=" O SER G 361 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN G 379 " --> pdb=" O MET G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 407 removed outlier: 3.535A pdb=" N ARG G 394 " --> pdb=" O ASP G 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.844A pdb=" N SER J 89 " --> pdb=" O GLN J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 112 Processing helix chain 'J' and resid 119 through 131 removed outlier: 3.648A pdb=" N PHE J 131 " --> pdb=" O LEU J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 169 removed outlier: 3.500A pdb=" N ASN J 159 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 190 removed outlier: 3.897A pdb=" N GLN J 185 " --> pdb=" O ALA J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 214 Processing helix chain 'J' and resid 218 through 222 Processing helix chain 'J' and resid 226 through 230 Processing helix chain 'J' and resid 243 through 255 Processing helix chain 'J' and resid 262 through 273 removed outlier: 4.084A pdb=" N ASP J 266 " --> pdb=" O GLU J 262 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY J 273 " --> pdb=" O PHE J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 279 removed outlier: 4.180A pdb=" N ALA J 278 " --> pdb=" O ASP J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 282 No H-bonds generated for 'chain 'J' and resid 280 through 282' Processing helix chain 'J' and resid 283 through 301 removed outlier: 3.501A pdb=" N ILE J 287 " --> pdb=" O ASP J 283 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA J 288 " --> pdb=" O TYR J 284 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE J 297 " --> pdb=" O GLN J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 324 removed outlier: 4.027A pdb=" N THR J 315 " --> pdb=" O ASP J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 337 Processing helix chain 'J' and resid 361 through 379 removed outlier: 3.901A pdb=" N ARG J 365 " --> pdb=" O SER J 361 " (cutoff:3.500A) Processing helix chain 'J' and resid 390 through 407 Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 143 removed outlier: 6.543A pdb=" N LEU A 94 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS A 140 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 96 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 142 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET A 98 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A 67 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 97 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 69 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLY A 99 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 66 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR A 176 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL A 68 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 175 " --> pdb=" O VAL A 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 260 Processing sheet with id=AA3, first strand: chain 'D' and resid 137 through 143 removed outlier: 6.396A pdb=" N GLY D 67 " --> pdb=" O HIS D 95 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE D 97 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 69 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N GLY D 99 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE D 66 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR D 176 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL D 68 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE D 175 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 259 through 260 removed outlier: 6.285A pdb=" N ARG D 232 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE D 308 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 234 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 233 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE D 343 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA D 235 " --> pdb=" O ILE D 343 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 345 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU D 237 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 137 through 143 removed outlier: 6.333A pdb=" N GLY G 67 " --> pdb=" O HIS G 95 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE G 97 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL G 69 " --> pdb=" O ILE G 97 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY G 99 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE G 66 " --> pdb=" O LEU G 174 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N TYR G 176 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL G 68 " --> pdb=" O TYR G 176 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE G 175 " --> pdb=" O VAL G 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 259 through 260 removed outlier: 3.513A pdb=" N ALA G 306 " --> pdb=" O ARG G 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 137 through 143 removed outlier: 6.576A pdb=" N LEU J 94 " --> pdb=" O ARG J 138 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N HIS J 140 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE J 96 " --> pdb=" O HIS J 140 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE J 142 " --> pdb=" O ILE J 96 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET J 98 " --> pdb=" O PHE J 142 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY J 67 " --> pdb=" O HIS J 95 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE J 97 " --> pdb=" O GLY J 67 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL J 69 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLY J 99 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE J 66 " --> pdb=" O LEU J 174 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR J 176 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL J 68 " --> pdb=" O TYR J 176 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE J 175 " --> pdb=" O VAL J 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'J' and resid 259 through 260 removed outlier: 3.554A pdb=" N ALA J 306 " --> pdb=" O ARG J 232 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR J 233 " --> pdb=" O LEU J 341 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE J 343 " --> pdb=" O THR J 233 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA J 235 " --> pdb=" O ILE J 343 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU J 345 " --> pdb=" O ALA J 235 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU J 237 " --> pdb=" O LEU J 345 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1956 1.31 - 1.44: 3356 1.44 - 1.56: 6468 1.56 - 1.69: 32 1.69 - 1.81: 84 Bond restraints: 11896 Sorted by residual: bond pdb=" C2D NAD G 601 " pdb=" C3D NAD G 601 " ideal model delta sigma weight residual 1.531 1.259 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C2D NAD J 601 " pdb=" C3D NAD J 601 " ideal model delta sigma weight residual 1.531 1.260 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.262 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C2D NAD D 601 " pdb=" C3D NAD D 601 " ideal model delta sigma weight residual 1.531 1.263 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C1B NAD D 601 " pdb=" C2B NAD D 601 " ideal model delta sigma weight residual 1.534 1.297 0.237 2.00e-02 2.50e+03 1.41e+02 ... (remaining 11891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 15922 2.81 - 5.62: 142 5.62 - 8.44: 42 8.44 - 11.25: 20 11.25 - 14.06: 14 Bond angle restraints: 16140 Sorted by residual: angle pdb=" C2N NAD A 601 " pdb=" C3N NAD A 601 " pdb=" C7N NAD A 601 " ideal model delta sigma weight residual 122.45 108.39 14.06 3.00e+00 1.11e-01 2.20e+01 angle pdb=" C2N NAD J 601 " pdb=" C3N NAD J 601 " pdb=" C7N NAD J 601 " ideal model delta sigma weight residual 122.45 108.53 13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C2N NAD D 601 " pdb=" C3N NAD D 601 " pdb=" C7N NAD D 601 " ideal model delta sigma weight residual 122.45 108.66 13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1A NAD D 601 " pdb=" PA NAD D 601 " pdb=" O2A NAD D 601 " ideal model delta sigma weight residual 122.64 108.90 13.74 3.00e+00 1.11e-01 2.10e+01 angle pdb=" O1A NAD G 601 " pdb=" PA NAD G 601 " pdb=" O2A NAD G 601 " ideal model delta sigma weight residual 122.64 108.92 13.72 3.00e+00 1.11e-01 2.09e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6214 17.88 - 35.76: 710 35.76 - 53.64: 151 53.64 - 71.51: 33 71.51 - 89.39: 28 Dihedral angle restraints: 7136 sinusoidal: 3076 harmonic: 4060 Sorted by residual: dihedral pdb=" CA ASP J 101 " pdb=" CB ASP J 101 " pdb=" CG ASP J 101 " pdb=" OD1 ASP J 101 " ideal model delta sinusoidal sigma weight residual -30.00 -88.67 58.67 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP G 101 " pdb=" CB ASP G 101 " pdb=" CG ASP G 101 " pdb=" OD1 ASP G 101 " ideal model delta sinusoidal sigma weight residual -30.00 -88.04 58.04 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP D 101 " pdb=" CB ASP D 101 " pdb=" CG ASP D 101 " pdb=" OD1 ASP D 101 " ideal model delta sinusoidal sigma weight residual -30.00 -87.15 57.15 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 7133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1506 0.072 - 0.145: 182 0.145 - 0.217: 5 0.217 - 0.289: 3 0.289 - 0.362: 4 Chirality restraints: 1700 Sorted by residual: chirality pdb=" C3D NAD D 601 " pdb=" C2D NAD D 601 " pdb=" C4D NAD D 601 " pdb=" O3D NAD D 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C3D NAD A 601 " pdb=" C2D NAD A 601 " pdb=" C4D NAD A 601 " pdb=" O3D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C3D NAD G 601 " pdb=" C2D NAD G 601 " pdb=" C4D NAD G 601 " pdb=" O3D NAD G 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1697 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD J 601 " 0.488 2.00e-02 2.50e+03 3.47e-01 2.41e+03 pdb=" C2N NAD J 601 " 0.082 2.00e-02 2.50e+03 pdb=" C3N NAD J 601 " -0.361 2.00e-02 2.50e+03 pdb=" C4N NAD J 601 " 0.213 2.00e-02 2.50e+03 pdb=" C5N NAD J 601 " 0.358 2.00e-02 2.50e+03 pdb=" C6N NAD J 601 " -0.507 2.00e-02 2.50e+03 pdb=" C7N NAD J 601 " 0.108 2.00e-02 2.50e+03 pdb=" N1N NAD J 601 " -0.381 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 601 " -0.176 2.00e-02 2.50e+03 2.49e-01 1.24e+03 pdb=" C2N NAD A 601 " 0.229 2.00e-02 2.50e+03 pdb=" C3N NAD A 601 " -0.355 2.00e-02 2.50e+03 pdb=" C4N NAD A 601 " 0.260 2.00e-02 2.50e+03 pdb=" C5N NAD A 601 " 0.004 2.00e-02 2.50e+03 pdb=" C6N NAD A 601 " -0.269 2.00e-02 2.50e+03 pdb=" C7N NAD A 601 " -0.071 2.00e-02 2.50e+03 pdb=" N1N NAD A 601 " 0.379 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD G 601 " -0.099 2.00e-02 2.50e+03 2.49e-01 1.24e+03 pdb=" C2N NAD G 601 " 0.166 2.00e-02 2.50e+03 pdb=" C3N NAD G 601 " -0.341 2.00e-02 2.50e+03 pdb=" C4N NAD G 601 " 0.328 2.00e-02 2.50e+03 pdb=" C5N NAD G 601 " 0.001 2.00e-02 2.50e+03 pdb=" C6N NAD G 601 " -0.327 2.00e-02 2.50e+03 pdb=" C7N NAD G 601 " -0.078 2.00e-02 2.50e+03 pdb=" N1N NAD G 601 " 0.351 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2011 2.77 - 3.30: 10555 3.30 - 3.83: 19351 3.83 - 4.37: 23099 4.37 - 4.90: 39428 Nonbonded interactions: 94444 Sorted by model distance: nonbonded pdb=" OD1 ASP D 311 " pdb=" N PHE D 312 " model vdw 2.235 3.120 nonbonded pdb=" OD1 ASP J 311 " pdb=" N PHE J 312 " model vdw 2.235 3.120 nonbonded pdb=" OD1 ASP A 311 " pdb=" N PHE A 312 " model vdw 2.243 3.120 nonbonded pdb=" O2D NAD D 601 " pdb=" O3D NAD D 601 " model vdw 2.260 2.432 nonbonded pdb=" OG1 THR A 224 " pdb=" O LYS A 300 " model vdw 2.280 3.040 ... (remaining 94439 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.160 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 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 : 0.013 0.272 11896 Z= 0.637 Angle : 0.842 14.059 16140 Z= 0.353 Chirality : 0.049 0.362 1700 Planarity : 0.013 0.347 2076 Dihedral : 16.528 89.392 4528 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.22), residues: 1380 helix: 0.89 (0.20), residues: 672 sheet: 1.54 (0.37), residues: 212 loop : -0.75 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 403 TYR 0.009 0.001 TYR A 176 PHE 0.011 0.001 PHE A 269 TRP 0.011 0.001 TRP A 154 HIS 0.004 0.001 HIS G 189 Details of bonding type rmsd covalent geometry : bond 0.01277 (11896) covalent geometry : angle 0.84187 (16140) hydrogen bonds : bond 0.17557 ( 524) hydrogen bonds : angle 7.29938 ( 1506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.457 Fit side-chains REVERT: D 261 TRP cc_start: 0.6715 (m-10) cc_final: 0.6335 (m-90) REVERT: G 89 SER cc_start: 0.8054 (p) cc_final: 0.7789 (m) REVERT: G 335 ASP cc_start: 0.6180 (m-30) cc_final: 0.5905 (m-30) outliers start: 0 outliers final: 2 residues processed: 298 average time/residue: 0.6990 time to fit residues: 221.5084 Evaluate side-chains 133 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain J residue 66 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D 370 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 ASN J 116 GLN J 189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.122320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.096115 restraints weight = 24142.349| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.42 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11896 Z= 0.189 Angle : 0.659 7.465 16140 Z= 0.348 Chirality : 0.046 0.152 1700 Planarity : 0.005 0.078 2076 Dihedral : 9.286 89.999 1760 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.37 % Allowed : 15.03 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.22), residues: 1380 helix: 1.41 (0.20), residues: 688 sheet: 0.48 (0.34), residues: 228 loop : -0.36 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 403 TYR 0.023 0.002 TYR J 150 PHE 0.017 0.002 PHE A 269 TRP 0.032 0.002 TRP G 157 HIS 0.007 0.002 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00422 (11896) covalent geometry : angle 0.65860 (16140) hydrogen bonds : bond 0.04730 ( 524) hydrogen bonds : angle 5.11833 ( 1506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: A 244 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7134 (ptmt) REVERT: A 262 GLU cc_start: 0.7489 (tt0) cc_final: 0.7172 (tt0) REVERT: A 406 MET cc_start: 0.8442 (mmm) cc_final: 0.8176 (mmm) REVERT: D 106 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7783 (ttm-80) REVERT: D 156 VAL cc_start: 0.8910 (t) cc_final: 0.8348 (t) REVERT: D 366 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8503 (mmtm) REVERT: G 335 ASP cc_start: 0.7121 (m-30) cc_final: 0.6548 (m-30) REVERT: G 381 ILE cc_start: 0.7561 (mm) cc_final: 0.7297 (mt) REVERT: G 389 GLU cc_start: 0.8351 (pm20) cc_final: 0.7590 (tm-30) REVERT: J 165 MET cc_start: 0.7269 (tmm) cc_final: 0.6844 (tmt) REVERT: J 225 GLU cc_start: 0.7234 (mp0) cc_final: 0.6977 (mp0) REVERT: J 261 TRP cc_start: 0.7308 (m-10) cc_final: 0.6061 (m-90) REVERT: J 388 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6675 (tp30) outliers start: 29 outliers final: 14 residues processed: 159 average time/residue: 0.6345 time to fit residues: 108.4598 Evaluate side-chains 130 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 388 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 126 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN G 85 GLN J 291 HIS ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.120963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095227 restraints weight = 24732.967| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 4.30 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11896 Z= 0.259 Angle : 0.716 7.258 16140 Z= 0.382 Chirality : 0.049 0.166 1700 Planarity : 0.006 0.064 2076 Dihedral : 8.914 77.251 1756 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.59 % Allowed : 17.16 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.22), residues: 1380 helix: 1.06 (0.20), residues: 688 sheet: -0.25 (0.34), residues: 204 loop : -0.17 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 325 TYR 0.023 0.002 TYR D 176 PHE 0.031 0.003 PHE D 329 TRP 0.013 0.002 TRP G 157 HIS 0.009 0.003 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00578 (11896) covalent geometry : angle 0.71632 (16140) hydrogen bonds : bond 0.05540 ( 524) hydrogen bonds : angle 5.11591 ( 1506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: A 165 MET cc_start: 0.7232 (pp-130) cc_final: 0.7001 (tmt) REVERT: A 193 GLU cc_start: 0.7414 (mp0) cc_final: 0.7134 (mp0) REVERT: A 244 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7291 (ptmt) REVERT: A 406 MET cc_start: 0.8444 (mmm) cc_final: 0.8174 (mmm) REVERT: D 106 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.8000 (ttm-80) REVERT: D 147 MET cc_start: 0.6594 (tpp) cc_final: 0.6363 (mmm) REVERT: D 244 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7310 (ptmt) REVERT: D 366 LYS cc_start: 0.8630 (mmtm) cc_final: 0.8212 (mmtm) REVERT: D 375 MET cc_start: 0.8370 (mtp) cc_final: 0.8099 (mtp) REVERT: G 165 MET cc_start: 0.7507 (tmm) cc_final: 0.7259 (tmt) REVERT: G 283 ASP cc_start: 0.7902 (m-30) cc_final: 0.7329 (OUTLIER) REVERT: G 335 ASP cc_start: 0.7116 (m-30) cc_final: 0.6582 (m-30) REVERT: G 385 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7740 (mtm-85) REVERT: G 389 GLU cc_start: 0.8300 (pm20) cc_final: 0.7896 (tm-30) REVERT: J 165 MET cc_start: 0.7385 (tmm) cc_final: 0.7012 (tmt) REVERT: J 182 ASP cc_start: 0.9113 (m-30) cc_final: 0.8899 (m-30) REVERT: J 204 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.6978 (tmm) REVERT: J 261 TRP cc_start: 0.7337 (m-10) cc_final: 0.6086 (m-90) REVERT: J 375 MET cc_start: 0.7760 (mtm) cc_final: 0.7498 (tmt) outliers start: 44 outliers final: 26 residues processed: 156 average time/residue: 0.6044 time to fit residues: 101.7567 Evaluate side-chains 136 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 97 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 189 HIS J 210 GLN ** J 316 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 = 0.3935 r_free = 0.3935 target = 0.120482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095038 restraints weight = 24548.890| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 4.26 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11896 Z= 0.242 Angle : 0.676 8.775 16140 Z= 0.360 Chirality : 0.048 0.167 1700 Planarity : 0.005 0.058 2076 Dihedral : 8.511 68.673 1756 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.33 % Allowed : 18.95 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.22), residues: 1380 helix: 0.98 (0.20), residues: 688 sheet: -0.47 (0.34), residues: 204 loop : -0.28 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 338 TYR 0.016 0.002 TYR G 176 PHE 0.035 0.003 PHE D 329 TRP 0.012 0.002 TRP G 157 HIS 0.015 0.003 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00540 (11896) covalent geometry : angle 0.67593 (16140) hydrogen bonds : bond 0.05092 ( 524) hydrogen bonds : angle 5.01213 ( 1506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: A 244 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7336 (ptmt) REVERT: A 387 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6855 (tp30) REVERT: D 147 MET cc_start: 0.7005 (tpp) cc_final: 0.6588 (mmm) REVERT: D 262 GLU cc_start: 0.7151 (tt0) cc_final: 0.6860 (tt0) REVERT: D 266 ASP cc_start: 0.8320 (m-30) cc_final: 0.8093 (m-30) REVERT: D 366 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8239 (mmtm) REVERT: D 375 MET cc_start: 0.8377 (mtp) cc_final: 0.7972 (mtp) REVERT: G 165 MET cc_start: 0.7491 (tmm) cc_final: 0.7281 (tmt) REVERT: G 193 GLU cc_start: 0.7547 (mp0) cc_final: 0.7307 (mp0) REVERT: G 283 ASP cc_start: 0.7820 (m-30) cc_final: 0.7463 (OUTLIER) REVERT: G 335 ASP cc_start: 0.7118 (m-30) cc_final: 0.6570 (m-30) REVERT: G 385 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7642 (mtm-85) REVERT: J 147 MET cc_start: 0.4387 (mmt) cc_final: 0.3995 (mmt) REVERT: J 165 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6981 (tmt) outliers start: 53 outliers final: 33 residues processed: 155 average time/residue: 0.5982 time to fit residues: 99.6531 Evaluate side-chains 138 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 53 optimal weight: 0.5980 chunk 98 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 115 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 316 GLN ** J 347 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.122608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096039 restraints weight = 24150.225| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 4.44 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11896 Z= 0.122 Angle : 0.540 7.862 16140 Z= 0.287 Chirality : 0.044 0.141 1700 Planarity : 0.004 0.057 2076 Dihedral : 8.112 66.346 1756 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.78 % Allowed : 22.06 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.22), residues: 1380 helix: 1.56 (0.20), residues: 688 sheet: -0.17 (0.34), residues: 204 loop : -0.23 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 106 TYR 0.011 0.001 TYR G 391 PHE 0.026 0.002 PHE D 329 TRP 0.008 0.001 TRP D 351 HIS 0.005 0.001 HIS D 77 Details of bonding type rmsd covalent geometry : bond 0.00267 (11896) covalent geometry : angle 0.54043 (16140) hydrogen bonds : bond 0.03875 ( 524) hydrogen bonds : angle 4.61440 ( 1506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: A 375 MET cc_start: 0.8259 (mtp) cc_final: 0.8012 (mtp) REVERT: D 147 MET cc_start: 0.7096 (tpp) cc_final: 0.6777 (mmm) REVERT: D 366 LYS cc_start: 0.8733 (mmtm) cc_final: 0.8310 (mmtm) REVERT: D 375 MET cc_start: 0.8391 (mtp) cc_final: 0.7903 (mtp) REVERT: G 283 ASP cc_start: 0.7701 (m-30) cc_final: 0.7373 (t0) REVERT: G 335 ASP cc_start: 0.7130 (m-30) cc_final: 0.6623 (m-30) REVERT: G 385 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7723 (mtm-85) REVERT: J 165 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6902 (tmt) REVERT: J 204 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7006 (tmm) REVERT: J 375 MET cc_start: 0.7769 (mtm) cc_final: 0.7507 (tmt) outliers start: 34 outliers final: 17 residues processed: 140 average time/residue: 0.6425 time to fit residues: 96.2203 Evaluate side-chains 123 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 204 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 88 optimal weight: 0.0470 chunk 18 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.122194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.095982 restraints weight = 24286.193| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 4.39 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11896 Z= 0.148 Angle : 0.566 8.435 16140 Z= 0.301 Chirality : 0.045 0.142 1700 Planarity : 0.004 0.052 2076 Dihedral : 7.992 66.386 1756 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.43 % Allowed : 21.90 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.22), residues: 1380 helix: 1.61 (0.20), residues: 688 sheet: -0.15 (0.34), residues: 204 loop : -0.24 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 106 TYR 0.011 0.001 TYR G 391 PHE 0.017 0.002 PHE D 329 TRP 0.006 0.001 TRP A 219 HIS 0.004 0.001 HIS D 77 Details of bonding type rmsd covalent geometry : bond 0.00338 (11896) covalent geometry : angle 0.56612 (16140) hydrogen bonds : bond 0.03986 ( 524) hydrogen bonds : angle 4.57275 ( 1506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: A 375 MET cc_start: 0.8294 (mtp) cc_final: 0.8007 (mtp) REVERT: D 147 MET cc_start: 0.7129 (tpp) cc_final: 0.6759 (mmm) REVERT: D 165 MET cc_start: 0.7513 (tmt) cc_final: 0.7227 (tmt) REVERT: D 204 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7273 (tmm) REVERT: D 366 LYS cc_start: 0.8750 (mmtm) cc_final: 0.8335 (mmtm) REVERT: D 375 MET cc_start: 0.8412 (mtp) cc_final: 0.8020 (mtp) REVERT: G 193 GLU cc_start: 0.7553 (mp0) cc_final: 0.7269 (mp0) REVERT: G 283 ASP cc_start: 0.7717 (m-30) cc_final: 0.7367 (t0) REVERT: G 335 ASP cc_start: 0.7104 (m-30) cc_final: 0.6586 (m-30) REVERT: G 385 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7716 (mtm-85) REVERT: J 165 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6910 (tmt) REVERT: J 375 MET cc_start: 0.7832 (mtm) cc_final: 0.7482 (tmm) REVERT: J 406 MET cc_start: 0.8549 (mmm) cc_final: 0.8205 (mmm) outliers start: 42 outliers final: 25 residues processed: 138 average time/residue: 0.6725 time to fit residues: 99.5543 Evaluate side-chains 131 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.122536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.094874 restraints weight = 24759.762| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 4.70 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11896 Z= 0.144 Angle : 0.568 9.146 16140 Z= 0.301 Chirality : 0.045 0.150 1700 Planarity : 0.004 0.052 2076 Dihedral : 7.892 67.344 1756 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.19 % Allowed : 22.71 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.23), residues: 1380 helix: 1.67 (0.20), residues: 688 sheet: -0.13 (0.34), residues: 204 loop : -0.23 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 385 TYR 0.011 0.001 TYR G 391 PHE 0.014 0.002 PHE D 329 TRP 0.006 0.001 TRP G 157 HIS 0.004 0.001 HIS D 77 Details of bonding type rmsd covalent geometry : bond 0.00327 (11896) covalent geometry : angle 0.56836 (16140) hydrogen bonds : bond 0.03863 ( 524) hydrogen bonds : angle 4.54023 ( 1506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: A 375 MET cc_start: 0.8309 (mtp) cc_final: 0.8045 (mtp) REVERT: A 406 MET cc_start: 0.8300 (mmm) cc_final: 0.8019 (mmm) REVERT: D 147 MET cc_start: 0.7126 (tpp) cc_final: 0.6795 (mmm) REVERT: D 204 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7315 (tmm) REVERT: D 366 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8339 (mmtm) REVERT: D 375 MET cc_start: 0.8405 (mtp) cc_final: 0.8018 (mtp) REVERT: D 400 GLU cc_start: 0.8353 (tp30) cc_final: 0.8151 (tp30) REVERT: G 193 GLU cc_start: 0.7593 (mp0) cc_final: 0.7364 (mp0) REVERT: G 283 ASP cc_start: 0.7656 (m-30) cc_final: 0.7357 (t0) REVERT: G 335 ASP cc_start: 0.7213 (m-30) cc_final: 0.6692 (m-30) REVERT: G 385 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7644 (mtm-85) REVERT: J 375 MET cc_start: 0.7823 (mtm) cc_final: 0.7623 (tmt) REVERT: J 406 MET cc_start: 0.8527 (mmm) cc_final: 0.8147 (mmm) outliers start: 39 outliers final: 26 residues processed: 140 average time/residue: 0.6324 time to fit residues: 95.3718 Evaluate side-chains 129 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 10 optimal weight: 0.0020 chunk 30 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 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 = 0.3974 r_free = 0.3974 target = 0.123239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.096955 restraints weight = 24128.402| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 4.39 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11896 Z= 0.120 Angle : 0.556 7.900 16140 Z= 0.295 Chirality : 0.044 0.138 1700 Planarity : 0.004 0.052 2076 Dihedral : 7.752 67.804 1756 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.61 % Allowed : 23.53 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.23), residues: 1380 helix: 1.76 (0.20), residues: 688 sheet: -0.07 (0.34), residues: 204 loop : -0.20 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 106 TYR 0.010 0.001 TYR G 391 PHE 0.033 0.002 PHE J 329 TRP 0.006 0.001 TRP G 157 HIS 0.005 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00272 (11896) covalent geometry : angle 0.55595 (16140) hydrogen bonds : bond 0.03592 ( 524) hydrogen bonds : angle 4.37585 ( 1506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: A 375 MET cc_start: 0.8330 (mtp) cc_final: 0.8050 (mtp) REVERT: A 406 MET cc_start: 0.8311 (mmm) cc_final: 0.8045 (mmm) REVERT: D 147 MET cc_start: 0.7141 (tpp) cc_final: 0.6823 (mmm) REVERT: D 193 GLU cc_start: 0.7582 (mp0) cc_final: 0.7311 (mp0) REVERT: D 204 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7279 (tmm) REVERT: D 366 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8370 (mmtm) REVERT: D 375 MET cc_start: 0.8407 (mtp) cc_final: 0.8121 (mtp) REVERT: D 406 MET cc_start: 0.8237 (mmm) cc_final: 0.7990 (mmm) REVERT: G 193 GLU cc_start: 0.7595 (mp0) cc_final: 0.7309 (mp0) REVERT: G 283 ASP cc_start: 0.7683 (m-30) cc_final: 0.7320 (t0) REVERT: G 335 ASP cc_start: 0.7155 (m-30) cc_final: 0.6641 (m-30) REVERT: G 385 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7745 (mtm-85) REVERT: J 375 MET cc_start: 0.7823 (mtm) cc_final: 0.7487 (tmm) outliers start: 32 outliers final: 21 residues processed: 132 average time/residue: 0.6627 time to fit residues: 94.1012 Evaluate side-chains 126 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 39 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 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 = 0.3960 r_free = 0.3960 target = 0.122423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097509 restraints weight = 23986.077| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 4.24 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11896 Z= 0.166 Angle : 0.609 8.723 16140 Z= 0.322 Chirality : 0.045 0.146 1700 Planarity : 0.004 0.051 2076 Dihedral : 7.791 68.528 1756 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.94 % Allowed : 23.53 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.22), residues: 1380 helix: 1.56 (0.20), residues: 688 sheet: -0.18 (0.34), residues: 204 loop : -0.29 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 106 TYR 0.018 0.001 TYR D 150 PHE 0.032 0.002 PHE J 329 TRP 0.005 0.001 TRP G 157 HIS 0.005 0.002 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00380 (11896) covalent geometry : angle 0.60930 (16140) hydrogen bonds : bond 0.04028 ( 524) hydrogen bonds : angle 4.50415 ( 1506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.6728 (mmm) cc_final: 0.5933 (mmm) REVERT: A 148 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: A 375 MET cc_start: 0.8330 (mtp) cc_final: 0.8065 (mtp) REVERT: D 147 MET cc_start: 0.7127 (tpp) cc_final: 0.6840 (mmm) REVERT: D 165 MET cc_start: 0.8110 (tmt) cc_final: 0.7866 (tmm) REVERT: D 193 GLU cc_start: 0.7542 (mp0) cc_final: 0.7275 (mp0) REVERT: D 204 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7278 (tmm) REVERT: D 366 LYS cc_start: 0.8762 (mmtm) cc_final: 0.8350 (mmtm) REVERT: D 375 MET cc_start: 0.8435 (mtp) cc_final: 0.7943 (mtp) REVERT: G 165 MET cc_start: 0.7821 (tmt) cc_final: 0.7586 (tmm) REVERT: G 193 GLU cc_start: 0.7641 (mp0) cc_final: 0.7356 (mp0) REVERT: G 283 ASP cc_start: 0.7656 (m-30) cc_final: 0.7299 (t0) REVERT: G 284 TYR cc_start: 0.7075 (m-80) cc_final: 0.6760 (m-80) REVERT: G 385 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7686 (mtm-85) REVERT: J 204 MET cc_start: 0.8216 (tmm) cc_final: 0.7804 (tmt) outliers start: 36 outliers final: 26 residues processed: 137 average time/residue: 0.6294 time to fit residues: 93.1929 Evaluate side-chains 137 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 135 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 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 = 0.3952 r_free = 0.3952 target = 0.121375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095926 restraints weight = 24330.593| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 4.35 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11896 Z= 0.188 Angle : 0.675 16.612 16140 Z= 0.351 Chirality : 0.046 0.150 1700 Planarity : 0.004 0.051 2076 Dihedral : 7.872 69.436 1756 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.78 % Allowed : 24.02 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.22), residues: 1380 helix: 1.43 (0.20), residues: 688 sheet: -0.26 (0.34), residues: 204 loop : -0.37 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 403 TYR 0.013 0.002 TYR J 176 PHE 0.033 0.002 PHE D 164 TRP 0.007 0.001 TRP G 157 HIS 0.005 0.002 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00428 (11896) covalent geometry : angle 0.67496 (16140) hydrogen bonds : bond 0.04260 ( 524) hydrogen bonds : angle 4.57150 ( 1506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: A 375 MET cc_start: 0.8351 (mtp) cc_final: 0.8092 (mtp) REVERT: D 147 MET cc_start: 0.7123 (tpp) cc_final: 0.6873 (mmm) REVERT: D 165 MET cc_start: 0.8041 (tmt) cc_final: 0.7824 (tmm) REVERT: D 193 GLU cc_start: 0.7538 (mp0) cc_final: 0.7277 (mp0) REVERT: D 204 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7326 (tmm) REVERT: D 206 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8436 (mm) REVERT: D 366 LYS cc_start: 0.8763 (mmtm) cc_final: 0.8339 (mmtm) REVERT: D 375 MET cc_start: 0.8447 (mtp) cc_final: 0.7998 (mtp) REVERT: D 400 GLU cc_start: 0.8322 (tp30) cc_final: 0.8116 (tp30) REVERT: G 147 MET cc_start: 0.4593 (mmm) cc_final: 0.1244 (ppp) REVERT: G 165 MET cc_start: 0.7478 (tmt) cc_final: 0.7273 (tmt) REVERT: G 193 GLU cc_start: 0.7558 (mp0) cc_final: 0.7291 (mp0) REVERT: G 283 ASP cc_start: 0.7658 (m-30) cc_final: 0.7314 (t0) REVERT: G 385 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7656 (mtm-85) REVERT: J 204 MET cc_start: 0.8185 (tmm) cc_final: 0.7775 (tmt) outliers start: 34 outliers final: 26 residues processed: 138 average time/residue: 0.6308 time to fit residues: 93.7530 Evaluate side-chains 135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 0.0030 chunk 131 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 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 = 0.3989 r_free = 0.3989 target = 0.123974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098512 restraints weight = 23942.613| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 4.30 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11896 Z= 0.112 Angle : 0.592 10.332 16140 Z= 0.308 Chirality : 0.044 0.142 1700 Planarity : 0.004 0.052 2076 Dihedral : 7.660 69.534 1756 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.47 % Allowed : 25.74 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.23), residues: 1380 helix: 1.82 (0.20), residues: 688 sheet: 0.29 (0.36), residues: 176 loop : -0.46 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 106 TYR 0.011 0.001 TYR J 391 PHE 0.028 0.002 PHE J 329 TRP 0.013 0.001 TRP G 157 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00252 (11896) covalent geometry : angle 0.59226 (16140) hydrogen bonds : bond 0.03299 ( 524) hydrogen bonds : angle 4.28796 ( 1506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3085.15 seconds wall clock time: 53 minutes 37.55 seconds (3217.55 seconds total)