Starting phenix.real_space_refine on Sun Dec 29 21:02:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7f_38098/12_2024/8x7f_38098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7f_38098/12_2024/8x7f_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_38098/12_2024/8x7f_38098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7f_38098/12_2024/8x7f_38098.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7f_38098/12_2024/8x7f_38098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7f_38098/12_2024/8x7f_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.33, per 1000 atoms: 0.72 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: 2.80 Conformation dependent library (CDL) restraints added in 1.5 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: 1.21 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: 3.55 Time building geometry restraints manager: 3.22 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: 0.00 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: 3.150 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.990 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.310 ------------------------------------------------------------------------------- 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= 0.795 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 *********************** 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 : 1.524 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: 1.5399 time to fit residues: 489.4097 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 : 1.473 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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= 0.326 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 *********************** 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 : 1.392 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6624 (mm) cc_final: 0.6420 (mt) REVERT: D 156 VAL cc_start: 0.8026 (t) cc_final: 0.7321 (t) REVERT: G 335 ASP cc_start: 0.6300 (m-30) cc_final: 0.6099 (m-30) REVERT: G 381 ILE cc_start: 0.7039 (mm) cc_final: 0.6775 (mt) REVERT: J 261 TRP cc_start: 0.6928 (m-10) cc_final: 0.6243 (m-90) outliers start: 39 outliers final: 15 residues processed: 163 average time/residue: 1.3892 time to fit residues: 243.9770 Evaluate side-chains 125 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET 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 68 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 0.0060 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- 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** J 210 GLN ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11896 Z= 0.215 Angle : 0.564 6.450 16140 Z= 0.302 Chirality : 0.044 0.141 1700 Planarity : 0.004 0.064 2076 Dihedral : 8.658 80.004 1756 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.78 % Allowed : 17.32 % Favored : 79.90 % 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: 1.08 (0.22), residues: 1380 helix: 1.56 (0.20), residues: 692 sheet: 0.39 (0.33), residues: 220 loop : -0.30 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 157 HIS 0.012 0.002 HIS A 152 PHE 0.020 0.002 PHE A 329 TYR 0.012 0.001 TYR G 391 ARG 0.005 0.000 ARG D 106 *********************** 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 159 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 HIS cc_start: 0.7152 (OUTLIER) cc_final: 0.6263 (m90) REVERT: A 381 ILE cc_start: 0.6625 (OUTLIER) cc_final: 0.6417 (mt) REVERT: A 387 GLU cc_start: 0.5923 (mm-30) cc_final: 0.5577 (tp30) REVERT: D 147 MET cc_start: 0.6063 (tpp) cc_final: 0.5723 (mmm) REVERT: D 283 ASP cc_start: 0.6122 (OUTLIER) cc_final: 0.5899 (m-30) REVERT: G 381 ILE cc_start: 0.6971 (mm) cc_final: 0.6711 (mt) REVERT: G 385 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6496 (mtm-85) outliers start: 34 outliers final: 16 residues processed: 148 average time/residue: 1.4086 time to fit residues: 224.5777 Evaluate side-chains 121 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 381 ILE 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 283 ASP Chi-restraints excluded: chain D residue 296 ASP 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 385 ARG Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 196 LEU 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 122 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 109 optimal weight: 0.0000 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 189 HIS ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11896 Z= 0.216 Angle : 0.569 7.463 16140 Z= 0.302 Chirality : 0.044 0.144 1700 Planarity : 0.004 0.064 2076 Dihedral : 8.292 71.688 1756 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.53 % Allowed : 18.87 % Favored : 78.59 % 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: 1.12 (0.22), residues: 1380 helix: 1.62 (0.20), residues: 692 sheet: 0.15 (0.33), residues: 228 loop : -0.17 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 157 HIS 0.004 0.001 HIS G 77 PHE 0.027 0.002 PHE D 329 TYR 0.012 0.001 TYR D 176 ARG 0.003 0.000 ARG J 125 *********************** 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 140 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 152 HIS cc_start: 0.7123 (OUTLIER) cc_final: 0.6018 (m90) REVERT: A 381 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6396 (mt) REVERT: G 385 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6472 (mtm-85) REVERT: J 192 ILE cc_start: 0.8164 (mm) cc_final: 0.7818 (mm) outliers start: 31 outliers final: 14 residues processed: 128 average time/residue: 1.4094 time to fit residues: 194.9669 Evaluate side-chains 110 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 381 ILE 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 196 LEU Chi-restraints excluded: chain G residue 89 SER 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 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 HIS J 291 HIS ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11896 Z= 0.323 Angle : 0.656 9.582 16140 Z= 0.348 Chirality : 0.047 0.155 1700 Planarity : 0.005 0.059 2076 Dihedral : 8.320 64.978 1756 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.51 % Allowed : 20.92 % Favored : 75.57 % 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: 1.26 (0.20), residues: 692 sheet: -0.24 (0.34), residues: 204 loop : -0.17 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 157 HIS 0.009 0.002 HIS D 152 PHE 0.027 0.003 PHE D 329 TYR 0.017 0.002 TYR J 176 ARG 0.004 0.001 ARG J 125 *********************** 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 147 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: A 152 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.5999 (m90) REVERT: A 381 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6460 (mt) REVERT: G 385 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6473 (mtm-85) REVERT: J 204 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6497 (tmm) outliers start: 43 outliers final: 22 residues processed: 134 average time/residue: 1.3218 time to fit residues: 192.1723 Evaluate side-chains 124 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 381 ILE 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 196 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 333 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 30.0000 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11896 Z= 0.167 Angle : 0.558 11.107 16140 Z= 0.294 Chirality : 0.044 0.150 1700 Planarity : 0.004 0.055 2076 Dihedral : 7.976 65.136 1756 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.45 % Allowed : 22.22 % Favored : 75.33 % 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: 1.10 (0.22), residues: 1380 helix: 1.63 (0.20), residues: 692 sheet: 0.04 (0.35), residues: 204 loop : -0.17 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 157 HIS 0.005 0.001 HIS G 77 PHE 0.029 0.002 PHE D 329 TYR 0.011 0.001 TYR G 391 ARG 0.007 0.000 ARG A 385 *********************** 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 128 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6405 (mt) REVERT: D 204 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6234 (tmm) REVERT: G 385 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6469 (mtm-85) REVERT: J 147 MET cc_start: 0.3725 (mmt) cc_final: 0.3182 (mmt) outliers start: 30 outliers final: 12 residues processed: 119 average time/residue: 1.4684 time to fit residues: 188.0883 Evaluate side-chains 102 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 381 ILE 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 204 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 196 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 131 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 171 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 379 ASN ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11896 Z= 0.270 Angle : 0.634 11.039 16140 Z= 0.335 Chirality : 0.046 0.184 1700 Planarity : 0.005 0.051 2076 Dihedral : 7.985 65.421 1756 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.02 % Allowed : 23.12 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.22), residues: 1380 helix: 1.41 (0.20), residues: 692 sheet: -0.04 (0.36), residues: 184 loop : -0.28 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.005 0.002 HIS G 80 PHE 0.022 0.002 PHE D 329 TYR 0.014 0.002 TYR J 176 ARG 0.006 0.001 ARG A 385 *********************** 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 138 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6154 (m90) REVERT: A 381 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6405 (mt) REVERT: G 244 LYS cc_start: 0.6561 (pmtt) cc_final: 0.6338 (pttt) REVERT: G 385 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6459 (mtm-85) REVERT: J 147 MET cc_start: 0.4261 (mmt) cc_final: 0.3787 (mmt) outliers start: 37 outliers final: 17 residues processed: 127 average time/residue: 1.5556 time to fit residues: 213.5160 Evaluate side-chains 113 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 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 78 optimal weight: 0.0870 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 119 optimal weight: 0.0980 chunk 125 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11896 Z= 0.162 Angle : 0.568 10.504 16140 Z= 0.299 Chirality : 0.044 0.147 1700 Planarity : 0.004 0.050 2076 Dihedral : 7.670 64.621 1756 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.96 % Allowed : 24.51 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.23), residues: 1380 helix: 1.75 (0.20), residues: 692 sheet: 0.27 (0.37), residues: 184 loop : -0.33 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 157 HIS 0.006 0.001 HIS A 327 PHE 0.017 0.001 PHE J 329 TYR 0.010 0.001 TYR G 391 ARG 0.008 0.000 ARG A 385 *********************** 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 138 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6368 (mt) REVERT: G 204 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6219 (tmm) REVERT: G 385 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6455 (mtm-85) REVERT: J 147 MET cc_start: 0.4485 (mmt) cc_final: 0.4220 (mmt) outliers start: 24 outliers final: 8 residues processed: 125 average time/residue: 1.5503 time to fit residues: 208.4107 Evaluate side-chains 102 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 115 optimal weight: 0.0370 chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11896 Z= 0.237 Angle : 0.634 9.333 16140 Z= 0.333 Chirality : 0.045 0.152 1700 Planarity : 0.004 0.047 2076 Dihedral : 7.664 64.820 1756 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.88 % Allowed : 25.41 % Favored : 72.71 % 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: 1.05 (0.23), residues: 1380 helix: 1.64 (0.20), residues: 692 sheet: 0.14 (0.36), residues: 184 loop : -0.34 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 261 HIS 0.006 0.001 HIS A 327 PHE 0.028 0.002 PHE D 164 TYR 0.012 0.001 TYR G 176 ARG 0.008 0.001 ARG A 385 *********************** 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 119 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6595 (OUTLIER) cc_final: 0.6374 (mt) REVERT: D 179 GLU cc_start: 0.6449 (mm-30) cc_final: 0.6142 (mm-30) REVERT: D 204 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6250 (tmm) REVERT: G 204 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6246 (tmm) REVERT: G 385 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6488 (mtm-85) REVERT: J 147 MET cc_start: 0.4689 (mmt) cc_final: 0.4403 (mmt) outliers start: 23 outliers final: 12 residues processed: 108 average time/residue: 1.4734 time to fit residues: 171.4834 Evaluate side-chains 107 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain J residue 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 78 optimal weight: 0.0370 chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- 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 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4862 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= 0.184 Angle : 0.622 11.728 16140 Z= 0.322 Chirality : 0.044 0.150 1700 Planarity : 0.004 0.048 2076 Dihedral : 7.564 66.006 1756 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.80 % Allowed : 25.65 % Favored : 72.55 % 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: 1.15 (0.23), residues: 1380 helix: 1.76 (0.20), residues: 692 sheet: 0.20 (0.36), residues: 184 loop : -0.35 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 157 HIS 0.005 0.001 HIS A 327 PHE 0.023 0.001 PHE D 164 TYR 0.010 0.001 TYR G 391 ARG 0.008 0.000 ARG A 385 ********************** 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 125 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6366 (mt) REVERT: D 179 GLU cc_start: 0.6456 (mm-30) cc_final: 0.6135 (mm-30) REVERT: D 204 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6236 (tmm) REVERT: G 147 MET cc_start: 0.3127 (mmm) cc_final: 0.1140 (ppp) REVERT: G 381 ILE cc_start: 0.6876 (mm) cc_final: 0.6651 (mt) REVERT: G 385 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6494 (mtm-85) outliers start: 22 outliers final: 11 residues processed: 114 average time/residue: 1.6318 time to fit residues: 198.8538 Evaluate side-chains 105 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 385 ARG 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 33 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 40.0000 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3974 r_free = 0.3974 target = 0.122876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096151 restraints weight = 24230.746| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 4.58 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11896 Z= 0.263 Angle : 0.672 10.487 16140 Z= 0.351 Chirality : 0.046 0.154 1700 Planarity : 0.004 0.046 2076 Dihedral : 7.604 66.677 1756 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.96 % Allowed : 26.23 % Favored : 71.81 % 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: 0.89 (0.22), residues: 1380 helix: 1.50 (0.20), residues: 692 sheet: 0.03 (0.36), residues: 184 loop : -0.39 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 157 HIS 0.005 0.002 HIS G 80 PHE 0.023 0.002 PHE D 164 TYR 0.030 0.002 TYR D 150 ARG 0.007 0.001 ARG A 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4134.53 seconds wall clock time: 75 minutes 6.30 seconds (4506.30 seconds total)