Starting phenix.real_space_refine on Wed Sep 17 23:44:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jq5_61723/09_2025/9jq5_61723_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jq5_61723/09_2025/9jq5_61723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jq5_61723/09_2025/9jq5_61723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jq5_61723/09_2025/9jq5_61723.map" model { file = "/net/cci-nas-00/data/ceres_data/9jq5_61723/09_2025/9jq5_61723_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jq5_61723/09_2025/9jq5_61723_trim.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.069 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 20 5.49 5 S 92 5.16 5 C 7676 2.51 5 N 2136 2.21 5 O 2328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12252 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2956 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 11, 'TRANS': 375} Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2956 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 11, 'TRANS': 375} Chain: "C" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2956 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 11, 'TRANS': 375} Chain: "D" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2956 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 11, 'TRANS': 375} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'FAD': 1, 'IVC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'FAD': 1, 'IVC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'FAD': 1, 'IVC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'FAD': 1, 'IVC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.99, per 1000 atoms: 0.24 Number of scatterers: 12252 At special positions: 0 Unit cell: (103.824, 104.648, 102.176, 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 92 16.00 P 20 15.00 O 2328 8.00 N 2136 7.00 C 7676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 524.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 14 sheets defined 59.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 removed outlier: 3.944A pdb=" N ASN A 11 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 32 removed outlier: 4.043A pdb=" N GLU A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.704A pdb=" N TYR A 69 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 70 " --> pdb=" O VAL A 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 70' Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.724A pdb=" N HIS A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 3.550A pdb=" N SER A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.525A pdb=" N GLU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 242 through 258 removed outlier: 3.533A pdb=" N LEU A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.680A pdb=" N LEU A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Proline residue: A 275 - end of helix removed outlier: 3.617A pdb=" N HIS A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 321 removed outlier: 3.565A pdb=" N LYS A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 350 removed outlier: 3.641A pdb=" N CYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 332 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.689A pdb=" N ILE A 356 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 369 removed outlier: 3.502A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.651A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 391 removed outlier: 3.736A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.953A pdb=" N ASN B 11 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 47 through 58 removed outlier: 3.518A pdb=" N PHE B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.760A pdb=" N HIS B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.507A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.567A pdb=" N LYS B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Proline residue: B 122 - end of helix removed outlier: 4.051A pdb=" N SER B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 removed outlier: 3.589A pdb=" N MET B 147 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 243 through 258 removed outlier: 4.056A pdb=" N SER B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 280 removed outlier: 3.846A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Proline residue: B 275 - end of helix Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.576A pdb=" N GLU B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 351 removed outlier: 3.742A pdb=" N ILE B 332 " --> pdb=" O CYS B 328 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.704A pdb=" N ILE B 356 " --> pdb=" O ASN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 369 removed outlier: 3.724A pdb=" N LEU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 373 Processing helix chain 'B' and resid 377 through 391 removed outlier: 3.786A pdb=" N PHE B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.708A pdb=" N ASN C 11 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 32 removed outlier: 3.546A pdb=" N GLU C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 75 through 90 removed outlier: 3.659A pdb=" N ALA C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.726A pdb=" N ARG C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 143 through 147 Processing helix chain 'C' and resid 243 through 258 removed outlier: 3.697A pdb=" N ARG C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 277 Proline residue: C 275 - end of helix Processing helix chain 'C' and resid 290 through 319 Processing helix chain 'C' and resid 324 through 351 removed outlier: 3.712A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 369 removed outlier: 3.720A pdb=" N LEU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 366 " --> pdb=" O GLY C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 373 Processing helix chain 'C' and resid 377 through 388 Processing helix chain 'D' and resid 8 through 12 removed outlier: 3.899A pdb=" N ASN D 11 " --> pdb=" O ASP D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 29 removed outlier: 3.601A pdb=" N GLN D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 35 through 43 Processing helix chain 'D' and resid 47 through 59 Processing helix chain 'D' and resid 75 through 86 removed outlier: 3.537A pdb=" N HIS D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 102 removed outlier: 3.610A pdb=" N GLY D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 143 through 147 removed outlier: 3.977A pdb=" N MET D 147 " --> pdb=" O VAL D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 191 Processing helix chain 'D' and resid 242 through 258 removed outlier: 4.358A pdb=" N VAL D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP D 252 " --> pdb=" O MET D 248 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 278 removed outlier: 3.781A pdb=" N LEU D 263 " --> pdb=" O ALA D 259 " (cutoff:3.500A) Proline residue: D 275 - end of helix removed outlier: 3.505A pdb=" N HIS D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 319 Processing helix chain 'D' and resid 324 through 351 removed outlier: 3.666A pdb=" N ILE D 332 " --> pdb=" O CYS D 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 369 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.739A pdb=" N ILE D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 392 removed outlier: 3.993A pdb=" N ASP D 392 " --> pdb=" O ALA D 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 4.286A pdb=" N ALA A 195 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 153 removed outlier: 5.971A pdb=" N TYR A 158 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A 230 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU A 160 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 228 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 162 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP A 166 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS A 222 " --> pdb=" O TRP A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.582A pdb=" N ALA B 132 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 179 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA B 195 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.950A pdb=" N LYS B 150 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 168 removed outlier: 4.324A pdb=" N TRP B 166 " --> pdb=" O CYS B 222 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N CYS B 222 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 134 removed outlier: 6.532A pdb=" N ALA C 132 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR C 179 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA C 134 " --> pdb=" O TYR C 179 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N LYS C 181 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA C 195 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 150 through 154 removed outlier: 3.602A pdb=" N LYS C 150 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 152 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR C 158 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS C 230 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU C 160 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TRP C 166 " --> pdb=" O CYS C 222 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS C 222 " --> pdb=" O TRP C 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AB2, first strand: chain 'D' and resid 131 through 134 removed outlier: 4.030A pdb=" N ALA D 195 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 150 through 153 removed outlier: 3.525A pdb=" N GLU D 152 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY D 162 " --> pdb=" O PHE D 226 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP D 166 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS D 222 " --> pdb=" O TRP D 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 150 through 153 removed outlier: 3.525A pdb=" N GLU D 152 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 281 through 282 655 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.29: 2041 1.29 - 1.45: 3237 1.45 - 1.61: 7034 1.61 - 1.76: 24 1.76 - 1.92: 148 Bond restraints: 12484 Sorted by residual: bond pdb=" C1 IVC A 401 " pdb=" C3 IVC A 401 " ideal model delta sigma weight residual 1.533 1.324 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C3 IVC D 401 " pdb=" O1 IVC D 401 " ideal model delta sigma weight residual 1.441 1.643 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C1 IVC C 401 " pdb=" C3 IVC C 401 " ideal model delta sigma weight residual 1.533 1.332 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C3 IVC B 401 " pdb=" O1 IVC B 401 " ideal model delta sigma weight residual 1.441 1.637 -0.196 2.00e-02 2.50e+03 9.62e+01 bond pdb=" C1 IVC B 401 " pdb=" C3 IVC B 401 " ideal model delta sigma weight residual 1.533 1.337 0.196 2.00e-02 2.50e+03 9.59e+01 ... (remaining 12479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 16619 4.15 - 8.29: 220 8.29 - 12.44: 43 12.44 - 16.58: 6 16.58 - 20.73: 4 Bond angle restraints: 16892 Sorted by residual: angle pdb=" N ALA D 33 " pdb=" CA ALA D 33 " pdb=" C ALA D 33 " ideal model delta sigma weight residual 109.81 125.34 -15.53 2.21e+00 2.05e-01 4.94e+01 angle pdb=" C21 IVC D 401 " pdb=" S1 IVC D 401 " pdb=" C22 IVC D 401 " ideal model delta sigma weight residual 100.81 121.54 -20.73 3.00e+00 1.11e-01 4.77e+01 angle pdb=" P2 IVC A 401 " pdb=" O7 IVC A 401 " pdb=" P3 IVC A 401 " ideal model delta sigma weight residual 137.80 117.24 20.56 3.00e+00 1.11e-01 4.70e+01 angle pdb=" C20 IVC D 401 " pdb=" C21 IVC D 401 " pdb=" S1 IVC D 401 " ideal model delta sigma weight residual 112.05 129.49 -17.44 3.00e+00 1.11e-01 3.38e+01 angle pdb=" P2 IVC B 401 " pdb=" O7 IVC B 401 " pdb=" P3 IVC B 401 " ideal model delta sigma weight residual 137.80 121.18 16.62 3.00e+00 1.11e-01 3.07e+01 ... (remaining 16887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 7137 18.05 - 36.09: 362 36.09 - 54.14: 138 54.14 - 72.18: 27 72.18 - 90.23: 8 Dihedral angle restraints: 7672 sinusoidal: 3308 harmonic: 4364 Sorted by residual: dihedral pdb=" C MET C 248 " pdb=" N MET C 248 " pdb=" CA MET C 248 " pdb=" CB MET C 248 " ideal model delta harmonic sigma weight residual -122.60 -134.40 11.80 0 2.50e+00 1.60e-01 2.23e+01 dihedral pdb=" N MET C 248 " pdb=" C MET C 248 " pdb=" CA MET C 248 " pdb=" CB MET C 248 " ideal model delta harmonic sigma weight residual 122.80 133.20 -10.40 0 2.50e+00 1.60e-01 1.73e+01 dihedral pdb=" C GLN D 37 " pdb=" N GLN D 37 " pdb=" CA GLN D 37 " pdb=" CB GLN D 37 " ideal model delta harmonic sigma weight residual -122.60 -130.99 8.39 0 2.50e+00 1.60e-01 1.13e+01 ... (remaining 7669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 1820 0.283 - 0.565: 3 0.565 - 0.848: 0 0.848 - 1.131: 0 1.131 - 1.413: 1 Chirality restraints: 1824 Sorted by residual: chirality pdb=" C2B FAD D 402 " pdb=" C1B FAD D 402 " pdb=" C3B FAD D 402 " pdb=" O2B FAD D 402 " both_signs ideal model delta sigma weight residual False -2.53 -1.12 -1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" CA MET C 248 " pdb=" N MET C 248 " pdb=" C MET C 248 " pdb=" CB MET C 248 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA MET B 135 " pdb=" N MET B 135 " pdb=" C MET B 135 " pdb=" CB MET B 135 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 1821 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD B 402 " -0.028 2.00e-02 2.50e+03 1.74e-02 1.44e+01 pdb=" C10 FAD B 402 " 0.002 2.00e-02 2.50e+03 pdb=" C2 FAD B 402 " 0.008 2.00e-02 2.50e+03 pdb=" C4 FAD B 402 " 0.007 2.00e-02 2.50e+03 pdb=" C4X FAD B 402 " 0.004 2.00e-02 2.50e+03 pdb=" C5X FAD B 402 " -0.048 2.00e-02 2.50e+03 pdb=" C6 FAD B 402 " -0.013 2.00e-02 2.50e+03 pdb=" C7 FAD B 402 " 0.007 2.00e-02 2.50e+03 pdb=" C7M FAD B 402 " -0.004 2.00e-02 2.50e+03 pdb=" C8 FAD B 402 " 0.011 2.00e-02 2.50e+03 pdb=" C8M FAD B 402 " 0.030 2.00e-02 2.50e+03 pdb=" C9 FAD B 402 " 0.024 2.00e-02 2.50e+03 pdb=" C9A FAD B 402 " -0.012 2.00e-02 2.50e+03 pdb=" N1 FAD B 402 " 0.003 2.00e-02 2.50e+03 pdb=" N10 FAD B 402 " -0.015 2.00e-02 2.50e+03 pdb=" N3 FAD B 402 " 0.018 2.00e-02 2.50e+03 pdb=" N5 FAD B 402 " -0.004 2.00e-02 2.50e+03 pdb=" O2 FAD B 402 " 0.004 2.00e-02 2.50e+03 pdb=" O4 FAD B 402 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 31 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C HIS D 31 " 0.064 2.00e-02 2.50e+03 pdb=" O HIS D 31 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU D 32 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 134 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C ALA B 134 " -0.064 2.00e-02 2.50e+03 pdb=" O ALA B 134 " 0.024 2.00e-02 2.50e+03 pdb=" N MET B 135 " 0.022 2.00e-02 2.50e+03 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1802 2.76 - 3.29: 12034 3.29 - 3.83: 20839 3.83 - 4.36: 25430 4.36 - 4.90: 44168 Nonbonded interactions: 104273 Sorted by model distance: nonbonded pdb=" OE1 GLU D 84 " pdb=" OH TYR D 312 " model vdw 2.221 3.040 nonbonded pdb=" O1 IVC A 401 " pdb=" O4 IVC A 401 " model vdw 2.249 2.432 nonbonded pdb=" OH TYR C 355 " pdb=" O ARG D 366 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR B 334 " pdb=" OH TYR C 334 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR B 324 " pdb=" OD2 ASP B 327 " model vdw 2.271 3.040 ... (remaining 104268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.130 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.440 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5150 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 : 0.010 0.209 12484 Z= 0.504 Angle : 1.105 20.726 16892 Z= 0.459 Chirality : 0.054 1.413 1824 Planarity : 0.004 0.063 2144 Dihedral : 12.681 90.226 4912 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.17 % Favored : 98.77 % Rotamer: Outliers : 1.38 % Allowed : 4.40 % Favored : 94.22 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.18), residues: 1540 helix: -0.75 (0.17), residues: 784 sheet: -1.15 (0.40), residues: 128 loop : -1.50 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 255 TYR 0.021 0.001 TYR C 245 PHE 0.006 0.000 PHE A 51 TRP 0.004 0.001 TRP B 52 HIS 0.002 0.000 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00984 (12484) covalent geometry : angle 1.10484 (16892) hydrogen bonds : bond 0.21503 ( 652) hydrogen bonds : angle 6.66064 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 406 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 418 average time/residue: 0.1336 time to fit residues: 77.0452 Evaluate side-chains 237 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 234 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 135 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 GLN A 29 GLN A 31 HIS A 47 ASN A 68 GLN A 111 ASN A 157 HIS A 161 ASN A 241 ASN A 294 GLN A 341 GLN B 31 HIS B 37 GLN B 68 GLN B 163 ASN B 278 HIS B 390 ASN C 19 GLN C 37 GLN C 54 GLN C 107 GLN C 241 ASN C 289 HIS ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN D 68 GLN D 107 GLN D 163 ASN D 291 GLN D 341 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.217753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.188767 restraints weight = 18150.649| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.67 r_work: 0.4198 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12484 Z= 0.212 Angle : 0.728 10.746 16892 Z= 0.356 Chirality : 0.046 0.252 1824 Planarity : 0.005 0.039 2144 Dihedral : 12.859 96.476 2136 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.01 % Allowed : 13.19 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.20), residues: 1540 helix: 0.03 (0.18), residues: 848 sheet: -1.20 (0.39), residues: 128 loop : -1.12 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 303 TYR 0.028 0.002 TYR A 310 PHE 0.015 0.002 PHE A 45 TRP 0.021 0.002 TRP A 166 HIS 0.007 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00475 (12484) covalent geometry : angle 0.72754 (16892) hydrogen bonds : bond 0.04972 ( 652) hydrogen bonds : angle 4.93354 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.8440 (mt0) cc_final: 0.8224 (mt0) REVERT: A 149 LEU cc_start: 0.6778 (tt) cc_final: 0.6547 (tt) REVERT: A 211 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7367 (pp) REVERT: B 22 GLN cc_start: 0.8126 (mm110) cc_final: 0.7923 (tp-100) REVERT: B 63 ILE cc_start: 0.5927 (OUTLIER) cc_final: 0.4859 (mt) REVERT: B 114 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6791 (pp20) REVERT: B 198 VAL cc_start: 0.6013 (t) cc_final: 0.5703 (m) REVERT: B 248 MET cc_start: 0.6080 (tpp) cc_final: 0.5806 (mtt) REVERT: B 303 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.5695 (tpp-160) REVERT: C 30 GLU cc_start: 0.6615 (tt0) cc_final: 0.5582 (tp30) REVERT: C 345 ASP cc_start: 0.6775 (m-30) cc_final: 0.6544 (m-30) REVERT: C 361 MET cc_start: 0.6990 (mmm) cc_final: 0.6761 (mmt) REVERT: D 202 MET cc_start: 0.3934 (ttm) cc_final: 0.3273 (tmm) outliers start: 37 outliers final: 17 residues processed: 265 average time/residue: 0.1117 time to fit residues: 42.7723 Evaluate side-chains 205 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN A 157 HIS B 163 ASN B 341 GLN C 37 GLN ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 220 ASN D 348 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.213494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.185573 restraints weight = 18175.652| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.40 r_work: 0.4183 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12484 Z= 0.167 Angle : 0.656 10.695 16892 Z= 0.319 Chirality : 0.043 0.204 1824 Planarity : 0.004 0.041 2144 Dihedral : 12.576 121.335 2128 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.75 % Allowed : 15.07 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.20), residues: 1540 helix: 0.57 (0.18), residues: 808 sheet: -0.95 (0.40), residues: 132 loop : -1.12 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 49 TYR 0.023 0.002 TYR A 310 PHE 0.020 0.002 PHE A 364 TRP 0.022 0.002 TRP A 166 HIS 0.013 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00381 (12484) covalent geometry : angle 0.65628 (16892) hydrogen bonds : bond 0.04539 ( 652) hydrogen bonds : angle 4.69517 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7558 (pp) REVERT: B 63 ILE cc_start: 0.5664 (OUTLIER) cc_final: 0.4895 (mt) REVERT: B 114 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6709 (pp20) REVERT: B 120 TYR cc_start: 0.6226 (m-80) cc_final: 0.6008 (m-80) REVERT: B 198 VAL cc_start: 0.6058 (t) cc_final: 0.5633 (m) REVERT: B 290 PHE cc_start: 0.7072 (m-80) cc_final: 0.6576 (m-80) REVERT: C 216 MET cc_start: 0.7353 (mmt) cc_final: 0.7083 (mmt) REVERT: D 202 MET cc_start: 0.4028 (ttm) cc_final: 0.3555 (tmm) REVERT: D 220 ASN cc_start: 0.6741 (OUTLIER) cc_final: 0.6454 (t0) REVERT: D 301 TYR cc_start: 0.6791 (t80) cc_final: 0.6348 (t80) outliers start: 46 outliers final: 21 residues processed: 250 average time/residue: 0.0987 time to fit residues: 37.1053 Evaluate side-chains 217 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 70 optimal weight: 0.0060 chunk 150 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.215505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.187597 restraints weight = 18307.116| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.46 r_work: 0.4203 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12484 Z= 0.121 Angle : 0.598 10.401 16892 Z= 0.290 Chirality : 0.041 0.177 1824 Planarity : 0.004 0.042 2144 Dihedral : 12.214 126.726 2128 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.52 % Allowed : 16.86 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.21), residues: 1540 helix: 0.85 (0.18), residues: 808 sheet: -0.92 (0.41), residues: 132 loop : -1.04 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.017 0.001 TYR A 310 PHE 0.033 0.001 PHE C 350 TRP 0.018 0.001 TRP A 166 HIS 0.006 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00264 (12484) covalent geometry : angle 0.59800 (16892) hydrogen bonds : bond 0.03904 ( 652) hydrogen bonds : angle 4.44991 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7387 (tpt) cc_final: 0.7060 (tpt) REVERT: A 157 HIS cc_start: 0.6455 (OUTLIER) cc_final: 0.6115 (m-70) REVERT: A 211 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7472 (pp) REVERT: B 63 ILE cc_start: 0.5565 (OUTLIER) cc_final: 0.5000 (mt) REVERT: B 290 PHE cc_start: 0.6961 (m-80) cc_final: 0.6479 (m-80) REVERT: B 309 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6906 (mp10) REVERT: C 216 MET cc_start: 0.7406 (mmt) cc_final: 0.7202 (mmt) REVERT: D 202 MET cc_start: 0.3818 (ttm) cc_final: 0.3461 (tmm) REVERT: D 217 ARG cc_start: 0.2413 (mtm180) cc_final: 0.2108 (mmm160) outliers start: 31 outliers final: 19 residues processed: 223 average time/residue: 0.0887 time to fit residues: 30.5090 Evaluate side-chains 206 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 TYR Chi-restraints excluded: chain D residue 385 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 123 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 19 optimal weight: 0.0170 chunk 141 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.217877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.191231 restraints weight = 18227.352| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 2.34 r_work: 0.4251 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12484 Z= 0.126 Angle : 0.594 10.582 16892 Z= 0.289 Chirality : 0.041 0.179 1824 Planarity : 0.004 0.043 2144 Dihedral : 11.877 135.729 2128 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.42 % Allowed : 17.10 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.21), residues: 1540 helix: 0.72 (0.18), residues: 840 sheet: -0.57 (0.41), residues: 140 loop : -0.96 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 49 TYR 0.016 0.001 TYR A 310 PHE 0.023 0.001 PHE C 350 TRP 0.041 0.002 TRP D 52 HIS 0.006 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00282 (12484) covalent geometry : angle 0.59421 (16892) hydrogen bonds : bond 0.03888 ( 652) hydrogen bonds : angle 4.36093 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7410 (tpt) cc_final: 0.7109 (tpt) REVERT: A 211 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7487 (pp) REVERT: A 305 MET cc_start: 0.6181 (mmm) cc_final: 0.5916 (mmm) REVERT: B 63 ILE cc_start: 0.5677 (OUTLIER) cc_final: 0.4881 (mt) REVERT: B 300 MET cc_start: 0.6859 (ttp) cc_final: 0.6146 (ptt) REVERT: C 226 PHE cc_start: 0.7300 (m-10) cc_final: 0.6935 (m-10) REVERT: D 40 ASP cc_start: 0.4605 (OUTLIER) cc_final: 0.4301 (t0) REVERT: D 179 TYR cc_start: 0.5341 (m-80) cc_final: 0.5127 (m-80) REVERT: D 202 MET cc_start: 0.3562 (ttm) cc_final: 0.3339 (tmm) REVERT: D 301 TYR cc_start: 0.6761 (t80) cc_final: 0.6307 (t80) outliers start: 42 outliers final: 25 residues processed: 233 average time/residue: 0.0995 time to fit residues: 35.1038 Evaluate side-chains 219 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN B 113 ASN B 116 GLN B 163 ASN B 169 ASN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.219228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.189684 restraints weight = 18756.326| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 2.55 r_work: 0.4264 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12484 Z= 0.183 Angle : 0.653 9.463 16892 Z= 0.319 Chirality : 0.043 0.193 1824 Planarity : 0.004 0.044 2144 Dihedral : 11.914 145.450 2128 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.09 % Allowed : 18.81 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.21), residues: 1540 helix: 0.67 (0.18), residues: 836 sheet: -1.02 (0.40), residues: 148 loop : -0.85 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 381 TYR 0.017 0.001 TYR D 97 PHE 0.021 0.002 PHE C 350 TRP 0.040 0.002 TRP D 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00420 (12484) covalent geometry : angle 0.65266 (16892) hydrogen bonds : bond 0.04340 ( 652) hydrogen bonds : angle 4.48959 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7618 (pp) REVERT: B 78 GLU cc_start: 0.6002 (mp0) cc_final: 0.5721 (pm20) REVERT: D 40 ASP cc_start: 0.4820 (OUTLIER) cc_final: 0.4403 (t0) REVERT: D 217 ARG cc_start: 0.2740 (mtm180) cc_final: 0.2328 (mmm160) REVERT: D 301 TYR cc_start: 0.7008 (t80) cc_final: 0.6453 (t80) REVERT: D 324 THR cc_start: 0.6170 (m) cc_final: 0.5916 (m) outliers start: 38 outliers final: 26 residues processed: 220 average time/residue: 0.0975 time to fit residues: 32.8932 Evaluate side-chains 211 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.217228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.187447 restraints weight = 18631.021| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 2.53 r_work: 0.4253 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12484 Z= 0.192 Angle : 0.688 9.988 16892 Z= 0.336 Chirality : 0.044 0.194 1824 Planarity : 0.004 0.046 2144 Dihedral : 12.016 151.170 2128 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.09 % Allowed : 19.63 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.21), residues: 1540 helix: 0.53 (0.18), residues: 836 sheet: -0.94 (0.40), residues: 148 loop : -0.93 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 363 TYR 0.019 0.002 TYR A 310 PHE 0.018 0.002 PHE A 205 TRP 0.041 0.003 TRP D 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00451 (12484) covalent geometry : angle 0.68789 (16892) hydrogen bonds : bond 0.04530 ( 652) hydrogen bonds : angle 4.57073 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7836 (pp) REVERT: C 86 ILE cc_start: 0.8470 (mm) cc_final: 0.8246 (mt) REVERT: D 301 TYR cc_start: 0.7073 (t80) cc_final: 0.6468 (t80) REVERT: D 324 THR cc_start: 0.6313 (m) cc_final: 0.6009 (m) outliers start: 38 outliers final: 28 residues processed: 209 average time/residue: 0.0925 time to fit residues: 29.6706 Evaluate side-chains 193 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 60 optimal weight: 0.0570 chunk 138 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.209228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.180375 restraints weight = 18457.751| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.39 r_work: 0.4188 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12484 Z= 0.157 Angle : 0.660 10.864 16892 Z= 0.326 Chirality : 0.043 0.193 1824 Planarity : 0.004 0.046 2144 Dihedral : 11.940 151.431 2128 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.44 % Allowed : 20.60 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.21), residues: 1540 helix: 0.58 (0.18), residues: 836 sheet: -0.96 (0.41), residues: 148 loop : -0.93 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 363 TYR 0.022 0.001 TYR D 97 PHE 0.020 0.002 PHE A 205 TRP 0.037 0.002 TRP D 52 HIS 0.004 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00370 (12484) covalent geometry : angle 0.66045 (16892) hydrogen bonds : bond 0.04247 ( 652) hydrogen bonds : angle 4.51638 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7806 (pp) REVERT: B 198 VAL cc_start: 0.6142 (t) cc_final: 0.5818 (m) REVERT: B 266 MET cc_start: 0.6329 (mtm) cc_final: 0.5890 (mtm) REVERT: C 86 ILE cc_start: 0.8390 (mm) cc_final: 0.8166 (mt) REVERT: D 301 TYR cc_start: 0.6955 (t80) cc_final: 0.6362 (t80) REVERT: D 324 THR cc_start: 0.6417 (m) cc_final: 0.6155 (m) outliers start: 30 outliers final: 24 residues processed: 204 average time/residue: 0.0987 time to fit residues: 30.4932 Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 51 optimal weight: 0.0170 chunk 117 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 136 optimal weight: 0.0270 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 HIS ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.210789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.181410 restraints weight = 18557.572| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.51 r_work: 0.4211 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12484 Z= 0.121 Angle : 0.626 11.840 16892 Z= 0.309 Chirality : 0.042 0.191 1824 Planarity : 0.004 0.046 2144 Dihedral : 11.705 150.670 2128 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.12 % Allowed : 21.09 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.21), residues: 1540 helix: 0.75 (0.18), residues: 836 sheet: -0.91 (0.41), residues: 148 loop : -0.90 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 363 TYR 0.023 0.001 TYR D 97 PHE 0.028 0.001 PHE D 364 TRP 0.034 0.002 TRP D 52 HIS 0.003 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00278 (12484) covalent geometry : angle 0.62630 (16892) hydrogen bonds : bond 0.03813 ( 652) hydrogen bonds : angle 4.36816 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7642 (pp) REVERT: B 81 LEU cc_start: 0.7811 (pp) cc_final: 0.7267 (tp) REVERT: B 198 VAL cc_start: 0.6125 (t) cc_final: 0.5856 (m) REVERT: C 30 GLU cc_start: 0.6195 (tt0) cc_final: 0.5925 (mt-10) REVERT: C 86 ILE cc_start: 0.8325 (mm) cc_final: 0.8074 (mt) REVERT: D 301 TYR cc_start: 0.6849 (t80) cc_final: 0.6244 (t80) REVERT: D 324 THR cc_start: 0.6459 (m) cc_final: 0.6225 (m) outliers start: 26 outliers final: 20 residues processed: 204 average time/residue: 0.0952 time to fit residues: 30.0876 Evaluate side-chains 197 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 27 optimal weight: 0.0270 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN ** C 322 HIS ** 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 = 0.4543 r_free = 0.4543 target = 0.205910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.176327 restraints weight = 18700.666| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.41 r_work: 0.4149 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12484 Z= 0.226 Angle : 0.756 11.992 16892 Z= 0.373 Chirality : 0.047 0.243 1824 Planarity : 0.005 0.061 2144 Dihedral : 11.978 159.515 2128 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.95 % Allowed : 21.74 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.21), residues: 1540 helix: 0.33 (0.18), residues: 836 sheet: -0.95 (0.42), residues: 148 loop : -0.99 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 382 TYR 0.030 0.002 TYR B 301 PHE 0.033 0.002 PHE D 364 TRP 0.040 0.003 TRP D 52 HIS 0.006 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00537 (12484) covalent geometry : angle 0.75636 (16892) hydrogen bonds : bond 0.04854 ( 652) hydrogen bonds : angle 4.72671 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LYS cc_start: 0.7567 (tppt) cc_final: 0.7336 (mmtt) REVERT: A 211 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7935 (pp) REVERT: B 24 MET cc_start: 0.7001 (mmt) cc_final: 0.6784 (mmt) REVERT: B 83 MET cc_start: 0.5625 (ppp) cc_final: 0.5267 (ppp) REVERT: C 30 GLU cc_start: 0.6286 (tt0) cc_final: 0.6016 (mt-10) REVERT: C 283 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6259 (t80) REVERT: D 324 THR cc_start: 0.6619 (m) cc_final: 0.6416 (m) outliers start: 24 outliers final: 19 residues processed: 190 average time/residue: 0.0974 time to fit residues: 28.4086 Evaluate side-chains 185 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 131 optimal weight: 0.0270 chunk 106 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.210343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.182029 restraints weight = 18800.618| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.46 r_work: 0.4183 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12484 Z= 0.139 Angle : 0.668 12.158 16892 Z= 0.328 Chirality : 0.044 0.265 1824 Planarity : 0.004 0.065 2144 Dihedral : 11.670 156.843 2128 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.28 % Allowed : 21.42 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.21), residues: 1540 helix: 0.59 (0.18), residues: 836 sheet: -0.96 (0.42), residues: 148 loop : -0.87 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 255 TYR 0.021 0.001 TYR D 301 PHE 0.029 0.002 PHE B 364 TRP 0.034 0.002 TRP D 52 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00327 (12484) covalent geometry : angle 0.66751 (16892) hydrogen bonds : bond 0.04090 ( 652) hydrogen bonds : angle 4.47631 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2589.31 seconds wall clock time: 45 minutes 23.87 seconds (2723.87 seconds total)