Starting phenix.real_space_refine on Tue Jul 29 13:50:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7f_38098/07_2025/8x7f_38098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7f_38098/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7f_38098/07_2025/8x7f_38098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7f_38098/07_2025/8x7f_38098.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7f_38098/07_2025/8x7f_38098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7f_38098/07_2025/8x7f_38098.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.11, per 1000 atoms: 0.70 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: 3.33 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.17 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: 3.42 Time building geometry restraints manager: 3.69 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: 0.03 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.810 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.950 ------------------------------------------------------------------------------- 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 : 6.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (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 TRP 0.011 0.001 TRP A 154 HIS 0.004 0.001 HIS G 189 PHE 0.011 0.001 PHE A 269 TYR 0.009 0.001 TYR A 176 ARG 0.001 0.000 ARG D 403 Details of bonding type rmsd hydrogen bonds : bond 0.17557 ( 524) hydrogen bonds : angle 7.29938 ( 1506) covalent geometry : bond 0.01277 (11896) covalent geometry : angle 0.84187 (16140) *********************** 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 : 1.305 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: 0.7788 (m) REVERT: G 335 ASP cc_start: 0.6180 (m-30) cc_final: 0.5903 (m-30) outliers start: 0 outliers final: 2 residues processed: 298 average time/residue: 1.6933 time to fit residues: 537.0874 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 : 1.766 ------------------------------------------------------------------------------- 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 114 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D 370 ASN G 85 GLN G 249 ASN J 116 GLN J 189 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.121661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.094272 restraints weight = 24224.341| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 4.54 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11896 Z= 0.228 Angle : 0.724 9.340 16140 Z= 0.381 Chirality : 0.048 0.147 1700 Planarity : 0.006 0.079 2076 Dihedral : 9.227 85.016 1760 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.19 % Allowed : 14.54 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1380 helix: 1.24 (0.20), residues: 684 sheet: 0.25 (0.34), residues: 228 loop : -0.32 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 157 HIS 0.009 0.002 HIS D 140 PHE 0.022 0.003 PHE G 229 TYR 0.023 0.002 TYR J 150 ARG 0.007 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 524) hydrogen bonds : angle 5.16933 ( 1506) covalent geometry : bond 0.00507 (11896) covalent geometry : angle 0.72381 (16140) *********************** 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 173 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: A 165 MET cc_start: 0.7282 (pp-130) cc_final: 0.7060 (tmm) REVERT: A 244 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7211 (ptmt) REVERT: A 406 MET cc_start: 0.8423 (mmm) cc_final: 0.8129 (mmm) REVERT: D 106 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7936 (ttm-80) REVERT: D 156 VAL cc_start: 0.8917 (t) cc_final: 0.8366 (t) REVERT: D 179 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: D 244 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7349 (ptmt) REVERT: G 335 ASP cc_start: 0.7155 (m-30) cc_final: 0.6626 (m-30) REVERT: G 381 ILE cc_start: 0.7582 (mm) cc_final: 0.7332 (mt) REVERT: G 389 GLU cc_start: 0.8325 (pm20) cc_final: 0.7856 (tp30) REVERT: J 165 MET cc_start: 0.7329 (tmm) cc_final: 0.6926 (tmt) REVERT: J 193 GLU cc_start: 0.7531 (mp0) cc_final: 0.7314 (mp0) REVERT: J 225 GLU cc_start: 0.7261 (mp0) cc_final: 0.7031 (mp0) REVERT: J 244 LYS cc_start: 0.7823 (pttp) cc_final: 0.7439 (ptmt) REVERT: J 253 ASN cc_start: 0.8712 (m-40) cc_final: 0.8485 (m-40) REVERT: J 261 TRP cc_start: 0.7336 (m-10) cc_final: 0.6045 (m-90) outliers start: 39 outliers final: 15 residues processed: 163 average time/residue: 2.0021 time to fit residues: 351.8358 Evaluate side-chains 132 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 91 VAL Chi-restraints excluded: chain D residue 179 GLU 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 120 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 91 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 333 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 17 optimal weight: 9.9990 chunk 96 optimal weight: 0.0970 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 210 GLN ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.121194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.095006 restraints weight = 24368.443| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 4.43 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11896 Z= 0.186 Angle : 0.601 8.009 16140 Z= 0.321 Chirality : 0.046 0.146 1700 Planarity : 0.005 0.063 2076 Dihedral : 8.736 78.542 1756 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.94 % Allowed : 17.08 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1380 helix: 1.38 (0.20), residues: 692 sheet: -0.11 (0.34), residues: 204 loop : -0.09 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 157 HIS 0.005 0.002 HIS D 140 PHE 0.023 0.002 PHE A 329 TYR 0.014 0.002 TYR G 176 ARG 0.005 0.001 ARG J 125 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 524) hydrogen bonds : angle 4.90083 ( 1506) covalent geometry : bond 0.00417 (11896) covalent geometry : angle 0.60083 (16140) *********************** 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 165 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: A 165 MET cc_start: 0.7180 (pp-130) cc_final: 0.6949 (tmt) REVERT: A 193 GLU cc_start: 0.7466 (mp0) cc_final: 0.7230 (mp0) REVERT: A 244 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7115 (ptmt) REVERT: A 262 GLU cc_start: 0.7340 (tt0) cc_final: 0.7079 (tt0) REVERT: A 406 MET cc_start: 0.8446 (mmm) cc_final: 0.8193 (mmm) REVERT: D 106 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7967 (ttm-80) REVERT: D 147 MET cc_start: 0.6811 (tpp) cc_final: 0.6519 (mmm) REVERT: D 179 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: D 244 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7391 (ptmt) REVERT: D 366 LYS cc_start: 0.8686 (mmtm) cc_final: 0.8251 (mmtm) REVERT: G 165 MET cc_start: 0.7520 (tmm) cc_final: 0.7277 (tmt) REVERT: G 283 ASP cc_start: 0.7852 (m-30) cc_final: 0.7360 (t0) REVERT: G 335 ASP cc_start: 0.7113 (m-30) cc_final: 0.6602 (m-30) REVERT: G 385 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7646 (mtm-85) REVERT: G 389 GLU cc_start: 0.8365 (pm20) cc_final: 0.7796 (tm-30) REVERT: J 165 MET cc_start: 0.7382 (tmm) cc_final: 0.6973 (tmt) REVERT: J 193 GLU cc_start: 0.7449 (mp0) cc_final: 0.7195 (mp0) REVERT: J 204 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.6996 (tmm) REVERT: J 225 GLU cc_start: 0.7338 (mp0) cc_final: 0.7097 (mp0) REVERT: J 253 ASN cc_start: 0.8654 (m-40) cc_final: 0.8451 (m-40) REVERT: J 261 TRP cc_start: 0.7328 (m-10) cc_final: 0.6080 (m-90) outliers start: 36 outliers final: 21 residues processed: 153 average time/residue: 1.4322 time to fit residues: 235.5556 Evaluate side-chains 135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 233 THR Chi-restraints excluded: chain A residue 244 LYS 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 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 333 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 91 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 204 MET Chi-restraints excluded: chain J residue 279 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.123308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096948 restraints weight = 23964.120| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 4.41 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11896 Z= 0.114 Angle : 0.523 6.624 16140 Z= 0.279 Chirality : 0.044 0.143 1700 Planarity : 0.004 0.056 2076 Dihedral : 8.160 70.644 1756 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.53 % Allowed : 18.30 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1380 helix: 1.73 (0.20), residues: 692 sheet: 0.20 (0.33), residues: 228 loop : -0.22 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 154 HIS 0.006 0.001 HIS D 152 PHE 0.024 0.002 PHE D 329 TYR 0.010 0.001 TYR G 391 ARG 0.005 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 524) hydrogen bonds : angle 4.55253 ( 1506) covalent geometry : bond 0.00248 (11896) covalent geometry : angle 0.52259 (16140) *********************** 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 159 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: A 165 MET cc_start: 0.7143 (pp-130) cc_final: 0.6930 (tmt) REVERT: A 193 GLU cc_start: 0.7410 (mp0) cc_final: 0.7088 (mp0) REVERT: A 244 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7291 (ptmt) REVERT: A 262 GLU cc_start: 0.7357 (tt0) cc_final: 0.7089 (tt0) REVERT: D 366 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8279 (mmtm) REVERT: D 375 MET cc_start: 0.8401 (mtp) cc_final: 0.8116 (mtp) REVERT: G 165 MET cc_start: 0.7502 (tmm) cc_final: 0.7301 (tmt) REVERT: G 283 ASP cc_start: 0.7699 (m-30) cc_final: 0.7174 (t0) REVERT: G 335 ASP cc_start: 0.7032 (m-30) cc_final: 0.6519 (m-30) REVERT: G 385 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7751 (mtm-85) REVERT: G 389 GLU cc_start: 0.8268 (pm20) cc_final: 0.7783 (tm-30) REVERT: J 165 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6965 (tmt) REVERT: J 193 GLU cc_start: 0.7428 (mp0) cc_final: 0.7143 (mp0) outliers start: 31 outliers final: 11 residues processed: 148 average time/residue: 1.4060 time to fit residues: 224.2390 Evaluate side-chains 114 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 244 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain G residue 120 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 165 MET Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 127 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 81 optimal weight: 0.0670 chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 HIS J 291 HIS J 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.124325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.097742 restraints weight = 23973.959| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 4.51 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11896 Z= 0.099 Angle : 0.509 9.318 16140 Z= 0.266 Chirality : 0.043 0.142 1700 Planarity : 0.004 0.052 2076 Dihedral : 7.864 68.168 1756 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.12 % Allowed : 20.59 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.23), residues: 1380 helix: 1.91 (0.20), residues: 692 sheet: 0.30 (0.35), residues: 204 loop : -0.01 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.005 0.001 HIS G 77 PHE 0.022 0.001 PHE D 329 TYR 0.010 0.001 TYR G 391 ARG 0.005 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 524) hydrogen bonds : angle 4.38070 ( 1506) covalent geometry : bond 0.00213 (11896) covalent geometry : angle 0.50876 (16140) *********************** 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 145 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: A 193 GLU cc_start: 0.7408 (mp0) cc_final: 0.7149 (mp0) REVERT: A 244 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7381 (ptmt) REVERT: A 262 GLU cc_start: 0.7370 (tt0) cc_final: 0.7087 (tt0) REVERT: A 375 MET cc_start: 0.8246 (mtp) cc_final: 0.7982 (mtp) REVERT: A 406 MET cc_start: 0.8400 (mmm) cc_final: 0.8195 (mmm) REVERT: D 375 MET cc_start: 0.8427 (mtp) cc_final: 0.8169 (mtp) REVERT: G 114 MET cc_start: 0.8178 (mtt) cc_final: 0.7965 (mtt) REVERT: G 283 ASP cc_start: 0.7538 (m-30) cc_final: 0.7029 (t0) REVERT: G 335 ASP cc_start: 0.6974 (m-30) cc_final: 0.6457 (m-30) REVERT: G 385 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7748 (mtm-85) REVERT: G 389 GLU cc_start: 0.8280 (pm20) cc_final: 0.7996 (tm-30) REVERT: J 147 MET cc_start: 0.3604 (mmt) cc_final: 0.3345 (tpt) REVERT: J 165 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6975 (tmt) REVERT: J 193 GLU cc_start: 0.7419 (mp0) cc_final: 0.7109 (mp0) REVERT: J 244 LYS cc_start: 0.7836 (pttp) cc_final: 0.7512 (ptmt) REVERT: J 375 MET cc_start: 0.7936 (mtm) cc_final: 0.7699 (mtp) outliers start: 26 outliers final: 9 residues processed: 136 average time/residue: 1.3628 time to fit residues: 199.8325 Evaluate side-chains 116 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU 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 244 LYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 283 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 123 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 chunk 129 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.124262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.097258 restraints weight = 24238.882| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 4.59 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4233 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= 0.112 Angle : 0.531 10.803 16140 Z= 0.278 Chirality : 0.044 0.148 1700 Planarity : 0.004 0.050 2076 Dihedral : 7.697 65.002 1756 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.53 % Allowed : 20.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.23), residues: 1380 helix: 1.94 (0.20), residues: 692 sheet: 0.35 (0.36), residues: 204 loop : -0.02 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 157 HIS 0.004 0.001 HIS G 77 PHE 0.018 0.002 PHE D 329 TYR 0.009 0.001 TYR D 176 ARG 0.007 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 524) hydrogen bonds : angle 4.33923 ( 1506) covalent geometry : bond 0.00255 (11896) covalent geometry : angle 0.53075 (16140) *********************** 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 141 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: A 193 GLU cc_start: 0.7453 (mp0) cc_final: 0.7138 (mp0) REVERT: A 244 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7387 (ptmt) REVERT: A 375 MET cc_start: 0.8260 (mtp) cc_final: 0.7998 (mtp) REVERT: D 375 MET cc_start: 0.8410 (mtp) cc_final: 0.8107 (mtp) REVERT: G 156 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8717 (t) REVERT: G 204 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7350 (tmm) REVERT: G 283 ASP cc_start: 0.7588 (m-30) cc_final: 0.7073 (t0) REVERT: G 335 ASP cc_start: 0.6993 (m-30) cc_final: 0.6455 (m-30) REVERT: G 389 GLU cc_start: 0.8329 (pm20) cc_final: 0.8060 (tm-30) REVERT: J 147 MET cc_start: 0.3774 (mmt) cc_final: 0.3404 (mmt) REVERT: J 165 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6934 (tmt) REVERT: J 192 ILE cc_start: 0.8468 (mm) cc_final: 0.7806 (mm) REVERT: J 193 GLU cc_start: 0.7418 (mp0) cc_final: 0.7095 (mp0) REVERT: J 375 MET cc_start: 0.8064 (mtm) cc_final: 0.7778 (mtp) outliers start: 31 outliers final: 13 residues processed: 129 average time/residue: 1.5466 time to fit residues: 215.0202 Evaluate side-chains 120 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 233 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 283 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 204 MET 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 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 63 optimal weight: 6.9990 chunk 127 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 134 optimal weight: 0.4980 chunk 75 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.124004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.097132 restraints weight = 24478.955| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 4.65 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11896 Z= 0.112 Angle : 0.527 10.507 16140 Z= 0.278 Chirality : 0.043 0.150 1700 Planarity : 0.004 0.049 2076 Dihedral : 7.545 62.014 1756 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.29 % Allowed : 21.41 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.23), residues: 1380 helix: 1.95 (0.20), residues: 692 sheet: 0.37 (0.36), residues: 204 loop : -0.04 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 157 HIS 0.004 0.001 HIS A 327 PHE 0.018 0.001 PHE D 329 TYR 0.009 0.001 TYR D 176 ARG 0.006 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 524) hydrogen bonds : angle 4.29469 ( 1506) covalent geometry : bond 0.00254 (11896) covalent geometry : angle 0.52724 (16140) *********************** 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 135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: A 172 PRO cc_start: 0.8775 (Cg_exo) cc_final: 0.8266 (Cg_endo) REVERT: A 193 GLU cc_start: 0.7442 (mp0) cc_final: 0.7148 (mp0) REVERT: A 244 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7404 (ptmt) REVERT: A 262 GLU cc_start: 0.7320 (tt0) cc_final: 0.6984 (tt0) REVERT: D 165 MET cc_start: 0.7527 (tmt) cc_final: 0.7190 (tmt) REVERT: D 204 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7257 (tmm) REVERT: D 366 LYS cc_start: 0.8726 (mmtm) cc_final: 0.8317 (mmtm) REVERT: D 375 MET cc_start: 0.8385 (mtp) cc_final: 0.8070 (mtp) REVERT: D 406 MET cc_start: 0.8266 (mmm) cc_final: 0.7954 (mmm) REVERT: G 193 GLU cc_start: 0.7512 (mp0) cc_final: 0.7212 (mp0) REVERT: G 335 ASP cc_start: 0.7088 (m-30) cc_final: 0.6583 (m-30) REVERT: J 147 MET cc_start: 0.3776 (mmt) cc_final: 0.3373 (mmt) REVERT: J 165 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6949 (tmt) REVERT: J 192 ILE cc_start: 0.8461 (mm) cc_final: 0.7851 (mm) REVERT: J 193 GLU cc_start: 0.7415 (mp0) cc_final: 0.7084 (mp0) outliers start: 28 outliers final: 16 residues processed: 123 average time/residue: 1.5877 time to fit residues: 210.4471 Evaluate side-chains 123 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 233 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 283 ASP Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 372 LEU 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 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 256 ASN G 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.122331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.095181 restraints weight = 24652.729| |-----------------------------------------------------------------------------| 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: 0.8088 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11896 Z= 0.187 Angle : 0.626 10.655 16140 Z= 0.329 Chirality : 0.046 0.162 1700 Planarity : 0.004 0.049 2076 Dihedral : 7.726 62.687 1756 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.86 % Allowed : 22.39 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1380 helix: 1.64 (0.20), residues: 692 sheet: 0.24 (0.37), residues: 184 loop : -0.12 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP G 261 HIS 0.006 0.002 HIS G 80 PHE 0.018 0.002 PHE G 329 TYR 0.015 0.002 TYR D 176 ARG 0.004 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 524) hydrogen bonds : angle 4.56189 ( 1506) covalent geometry : bond 0.00421 (11896) covalent geometry : angle 0.62587 (16140) *********************** 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 140 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.565 Fit side-chains REVERT: A 147 MET cc_start: 0.5256 (tpt) cc_final: 0.4785 (tpt) REVERT: A 148 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: A 193 GLU cc_start: 0.7462 (mp0) cc_final: 0.7153 (mp0) REVERT: A 244 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7233 (ptmt) REVERT: A 262 GLU cc_start: 0.7215 (tt0) cc_final: 0.6829 (tt0) REVERT: A 375 MET cc_start: 0.8308 (mtp) cc_final: 0.8011 (mtp) REVERT: A 406 MET cc_start: 0.8225 (mmm) cc_final: 0.7996 (mmm) REVERT: D 366 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8274 (mmtm) REVERT: D 375 MET cc_start: 0.8406 (mtp) cc_final: 0.8101 (mtp) REVERT: G 193 GLU cc_start: 0.7532 (mp0) cc_final: 0.7300 (mp0) REVERT: G 335 ASP cc_start: 0.7114 (m-30) cc_final: 0.6577 (m-30) REVERT: G 389 GLU cc_start: 0.8503 (pm20) cc_final: 0.8236 (tm-30) REVERT: J 147 MET cc_start: 0.4174 (mmt) cc_final: 0.3747 (mmt) REVERT: J 165 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7009 (tmt) REVERT: J 192 ILE cc_start: 0.8451 (mm) cc_final: 0.7885 (mm) REVERT: J 193 GLU cc_start: 0.7436 (mp0) cc_final: 0.7132 (mp0) REVERT: J 375 MET cc_start: 0.8096 (mtm) cc_final: 0.7540 (mpp) outliers start: 35 outliers final: 19 residues processed: 127 average time/residue: 1.5558 time to fit residues: 213.7795 Evaluate side-chains 118 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 233 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 120 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 G residue 69 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 283 ASP 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 254 ILE 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 98 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.123591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097066 restraints weight = 24193.179| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 4.55 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4644 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= 0.123 Angle : 0.576 9.917 16140 Z= 0.304 Chirality : 0.044 0.154 1700 Planarity : 0.004 0.051 2076 Dihedral : 7.586 64.382 1756 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.04 % Allowed : 23.45 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1380 helix: 1.78 (0.20), residues: 692 sheet: 0.29 (0.37), residues: 184 loop : -0.17 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 157 HIS 0.005 0.001 HIS A 327 PHE 0.014 0.001 PHE D 329 TYR 0.009 0.001 TYR D 284 ARG 0.004 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 524) hydrogen bonds : angle 4.35901 ( 1506) covalent geometry : bond 0.00282 (11896) covalent geometry : angle 0.57572 (16140) *********************** 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 130 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 2.727 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.5319 (tpt) cc_final: 0.5000 (tpt) REVERT: A 148 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: A 193 GLU cc_start: 0.7439 (mp0) cc_final: 0.7129 (mp0) REVERT: A 244 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7352 (ptmt) REVERT: A 262 GLU cc_start: 0.7279 (tt0) cc_final: 0.6966 (tt0) REVERT: A 375 MET cc_start: 0.8316 (mtp) cc_final: 0.8028 (mtp) REVERT: D 165 MET cc_start: 0.7492 (tmt) cc_final: 0.7272 (tmt) REVERT: D 253 ASN cc_start: 0.8632 (m-40) cc_final: 0.8396 (m-40) REVERT: D 374 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8880 (mt-10) REVERT: D 375 MET cc_start: 0.8398 (mtp) cc_final: 0.7874 (mtp) REVERT: D 406 MET cc_start: 0.8264 (mmm) cc_final: 0.7921 (mmm) REVERT: G 165 MET cc_start: 0.7482 (tmt) cc_final: 0.7121 (tpp) REVERT: G 193 GLU cc_start: 0.7552 (mp0) cc_final: 0.7259 (mp0) REVERT: G 335 ASP cc_start: 0.7110 (m-30) cc_final: 0.6590 (m-30) REVERT: G 389 GLU cc_start: 0.8521 (pm20) cc_final: 0.8157 (tm-30) REVERT: J 147 MET cc_start: 0.4113 (mmt) cc_final: 0.3736 (mmt) REVERT: J 192 ILE cc_start: 0.8466 (mm) cc_final: 0.7881 (mm) REVERT: J 193 GLU cc_start: 0.7430 (mp0) cc_final: 0.7099 (mp0) outliers start: 25 outliers final: 13 residues processed: 123 average time/residue: 2.0411 time to fit residues: 272.4625 Evaluate side-chains 112 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 196 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 196 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.121212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.094969 restraints weight = 24528.872| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.47 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11896 Z= 0.238 Angle : 0.707 9.382 16140 Z= 0.374 Chirality : 0.048 0.173 1700 Planarity : 0.005 0.049 2076 Dihedral : 7.831 63.292 1756 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.88 % Allowed : 23.77 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1380 helix: 1.12 (0.20), residues: 692 sheet: -0.08 (0.35), residues: 204 loop : -0.27 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 126 HIS 0.008 0.002 HIS G 80 PHE 0.019 0.002 PHE G 229 TYR 0.018 0.002 TYR G 176 ARG 0.009 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 524) hydrogen bonds : angle 4.71214 ( 1506) covalent geometry : bond 0.00534 (11896) covalent geometry : angle 0.70733 (16140) ********************** 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 126 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 2.535 Fit side-chains REVERT: A 148 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: A 193 GLU cc_start: 0.7397 (mp0) cc_final: 0.7111 (mp0) REVERT: A 244 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7139 (ptmt) REVERT: A 375 MET cc_start: 0.8364 (mtp) cc_final: 0.8074 (mtp) REVERT: A 406 MET cc_start: 0.8142 (mmm) cc_final: 0.7936 (mmm) REVERT: D 165 MET cc_start: 0.7513 (tmt) cc_final: 0.7236 (tmt) REVERT: D 204 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7300 (tmm) REVERT: D 366 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8251 (mmtm) REVERT: D 375 MET cc_start: 0.8393 (mtp) cc_final: 0.8092 (mtp) REVERT: D 385 ARG cc_start: 0.8540 (mtt180) cc_final: 0.8079 (mtp180) REVERT: G 165 MET cc_start: 0.7527 (tmt) cc_final: 0.7233 (tmm) REVERT: G 193 GLU cc_start: 0.7539 (mp0) cc_final: 0.7259 (mp0) REVERT: G 335 ASP cc_start: 0.7204 (m-30) cc_final: 0.6650 (m-30) REVERT: G 381 ILE cc_start: 0.7578 (mm) cc_final: 0.7350 (mt) REVERT: G 389 GLU cc_start: 0.8540 (pm20) cc_final: 0.8195 (tm-30) REVERT: J 193 GLU cc_start: 0.7459 (mp0) cc_final: 0.7156 (mp0) outliers start: 23 outliers final: 17 residues processed: 119 average time/residue: 1.6069 time to fit residues: 207.2636 Evaluate side-chains 119 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 233 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain D residue 120 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 156 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 283 ASP 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 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 4 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.121869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095673 restraints weight = 24464.135| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 4.52 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11896 Z= 0.171 Angle : 0.639 8.593 16140 Z= 0.337 Chirality : 0.046 0.165 1700 Planarity : 0.004 0.049 2076 Dihedral : 7.755 63.873 1756 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.63 % Allowed : 24.18 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1380 helix: 1.30 (0.20), residues: 692 sheet: -0.03 (0.36), residues: 184 loop : -0.35 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 157 HIS 0.005 0.002 HIS G 80 PHE 0.038 0.002 PHE J 329 TYR 0.013 0.001 TYR A 176 ARG 0.008 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 524) hydrogen bonds : angle 4.53636 ( 1506) covalent geometry : bond 0.00390 (11896) covalent geometry : angle 0.63893 (16140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7378.13 seconds wall clock time: 136 minutes 24.14 seconds (8184.14 seconds total)