Starting phenix.real_space_refine on Wed Jul 30 11:22:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jq5_61723/07_2025/9jq5_61723_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jq5_61723/07_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_61723/07_2025/9jq5_61723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jq5_61723/07_2025/9jq5_61723.map" model { file = "/net/cci-nas-00/data/ceres_data/9jq5_61723/07_2025/9jq5_61723_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jq5_61723/07_2025/9jq5_61723_trim.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.56, per 1000 atoms: 0.62 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: 2.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.72 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: 3.70 Time building geometry restraints manager: 3.46 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: 0.06 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: 1.190 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.270 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- 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 : 12.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (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 TRP 0.004 0.001 TRP B 52 HIS 0.002 0.000 HIS A 100 PHE 0.006 0.000 PHE A 51 TYR 0.021 0.001 TYR C 245 ARG 0.002 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.21503 ( 652) hydrogen bonds : angle 6.66064 ( 1875) covalent geometry : bond 0.00984 (12484) covalent geometry : angle 1.10484 (16892) *********************** 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 : 1.270 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: 0.2793 time to fit residues: 161.1005 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 : 1.391 ------------------------------------------------------------------------------- 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 128 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.0270 chunk 138 optimal weight: 7.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 241 ASN C 289 HIS ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN D 68 GLN D 106 ASN 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 = 0.4544 r_free = 0.4544 target = 0.209246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.179060 restraints weight = 18328.738| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.58 r_work: 0.4102 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 12484 Z= 0.314 Angle : 0.881 11.296 16892 Z= 0.435 Chirality : 0.052 0.222 1824 Planarity : 0.006 0.056 2144 Dihedral : 13.294 111.029 2136 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.91 % Allowed : 14.17 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1540 helix: -0.34 (0.17), residues: 840 sheet: -1.16 (0.39), residues: 132 loop : -1.03 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 166 HIS 0.013 0.002 HIS C 100 PHE 0.025 0.003 PHE A 45 TYR 0.032 0.003 TYR A 310 ARG 0.006 0.001 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.05960 ( 652) hydrogen bonds : angle 5.32485 ( 1875) covalent geometry : bond 0.00697 (12484) covalent geometry : angle 0.88083 (16892) *********************** 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 280 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.7250 (mt) cc_final: 0.6737 (mt) REVERT: A 149 LEU cc_start: 0.7036 (tt) cc_final: 0.6790 (tt) REVERT: A 161 ASN cc_start: 0.5669 (m110) cc_final: 0.5234 (t0) REVERT: A 211 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7631 (pp) REVERT: A 228 ASP cc_start: 0.6915 (t0) cc_final: 0.6575 (t0) REVERT: B 63 ILE cc_start: 0.5906 (OUTLIER) cc_final: 0.4935 (mt) REVERT: B 78 GLU cc_start: 0.6551 (mp0) cc_final: 0.6340 (mp0) REVERT: B 114 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6792 (pp20) REVERT: B 198 VAL cc_start: 0.6224 (t) cc_final: 0.5875 (m) REVERT: B 248 MET cc_start: 0.6240 (tpp) cc_final: 0.6019 (mtt) REVERT: B 303 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5828 (tpp-160) REVERT: B 361 MET cc_start: 0.7308 (tpp) cc_final: 0.6190 (mmm) REVERT: C 248 MET cc_start: 0.6419 (ttm) cc_final: 0.6004 (ttm) REVERT: C 345 ASP cc_start: 0.7157 (m-30) cc_final: 0.6862 (m-30) REVERT: D 118 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6372 (tp30) REVERT: D 199 GLU cc_start: 0.6926 (tp30) cc_final: 0.6463 (pm20) REVERT: D 301 TYR cc_start: 0.6977 (t80) cc_final: 0.6551 (t80) REVERT: D 369 LYS cc_start: 0.4738 (tmtt) cc_final: 0.4021 (tppt) outliers start: 48 outliers final: 22 residues processed: 268 average time/residue: 0.2327 time to fit residues: 91.9405 Evaluate side-chains 205 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP 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 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 165 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 287 ILE 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 Chi-restraints excluded: chain D residue 385 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN C 107 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 348 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.219486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.190130 restraints weight = 18710.819| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.56 r_work: 0.4307 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.4873 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= 0.166 Angle : 0.656 9.577 16892 Z= 0.321 Chirality : 0.043 0.207 1824 Planarity : 0.004 0.043 2144 Dihedral : 12.725 135.359 2128 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.50 % Allowed : 16.04 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1540 helix: 0.30 (0.18), residues: 796 sheet: -0.91 (0.38), residues: 140 loop : -1.07 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 166 HIS 0.006 0.001 HIS D 31 PHE 0.032 0.002 PHE C 350 TYR 0.022 0.002 TYR A 310 ARG 0.006 0.001 ARG C 366 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 652) hydrogen bonds : angle 4.81812 ( 1875) covalent geometry : bond 0.00381 (12484) covalent geometry : angle 0.65629 (16892) *********************** 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 242 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7672 (pp) REVERT: B 63 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5201 (mt) REVERT: B 198 VAL cc_start: 0.6043 (t) cc_final: 0.5756 (m) REVERT: D 220 ASN cc_start: 0.6566 (OUTLIER) cc_final: 0.6315 (t0) REVERT: D 301 TYR cc_start: 0.6964 (t80) cc_final: 0.6406 (t80) REVERT: D 369 LYS cc_start: 0.4761 (tmtt) cc_final: 0.3892 (tppt) outliers start: 43 outliers final: 21 residues processed: 231 average time/residue: 0.2680 time to fit residues: 94.9217 Evaluate side-chains 200 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 101 SER 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 223 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 107 GLN 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 377 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 93 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 43 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN B 163 ASN C 107 GLN ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.219971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.190690 restraints weight = 18494.126| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 2.53 r_work: 0.4350 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12484 Z= 0.148 Angle : 0.626 10.610 16892 Z= 0.306 Chirality : 0.042 0.191 1824 Planarity : 0.004 0.044 2144 Dihedral : 12.396 140.335 2128 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.50 % Allowed : 16.53 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1540 helix: 0.48 (0.18), residues: 800 sheet: -0.76 (0.39), residues: 140 loop : -0.99 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 166 HIS 0.005 0.001 HIS B 278 PHE 0.018 0.001 PHE D 205 TYR 0.018 0.001 TYR A 310 ARG 0.005 0.000 ARG C 366 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 652) hydrogen bonds : angle 4.63017 ( 1875) covalent geometry : bond 0.00340 (12484) covalent geometry : angle 0.62634 (16892) *********************** 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 236 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7676 (pp) REVERT: B 63 ILE cc_start: 0.5775 (OUTLIER) cc_final: 0.5173 (mt) REVERT: B 81 LEU cc_start: 0.7698 (pp) cc_final: 0.7235 (tp) REVERT: B 198 VAL cc_start: 0.6115 (t) cc_final: 0.5856 (m) outliers start: 43 outliers final: 27 residues processed: 226 average time/residue: 0.2170 time to fit residues: 75.3481 Evaluate side-chains 201 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 370 LEU 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 B residue 318 CYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 247 LEU 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 C residue 378 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN B 116 GLN B 163 ASN C 107 GLN ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.219374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.190078 restraints weight = 18491.987| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 2.53 r_work: 0.4338 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.5407 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= 0.158 Angle : 0.638 10.672 16892 Z= 0.311 Chirality : 0.042 0.202 1824 Planarity : 0.004 0.045 2144 Dihedral : 12.223 144.721 2128 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.18 % Allowed : 18.57 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1540 helix: 0.64 (0.18), residues: 816 sheet: -0.77 (0.40), residues: 140 loop : -0.87 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 52 HIS 0.006 0.001 HIS B 278 PHE 0.015 0.001 PHE B 364 TYR 0.017 0.001 TYR A 310 ARG 0.005 0.000 ARG C 366 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 652) hydrogen bonds : angle 4.59449 ( 1875) covalent geometry : bond 0.00365 (12484) covalent geometry : angle 0.63770 (16892) *********************** 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 226 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7348 (mttt) cc_final: 0.7144 (mttp) REVERT: A 211 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7860 (pp) REVERT: B 63 ILE cc_start: 0.5782 (OUTLIER) cc_final: 0.5205 (mt) REVERT: B 81 LEU cc_start: 0.7760 (pp) cc_final: 0.7282 (tp) REVERT: B 198 VAL cc_start: 0.6088 (t) cc_final: 0.5743 (m) REVERT: B 300 MET cc_start: 0.6850 (ttp) cc_final: 0.6047 (ptt) REVERT: C 86 ILE cc_start: 0.8390 (mm) cc_final: 0.8163 (mt) REVERT: D 202 MET cc_start: 0.3237 (tmm) cc_final: 0.2907 (tmm) outliers start: 39 outliers final: 24 residues processed: 214 average time/residue: 0.3196 time to fit residues: 106.3291 Evaluate side-chains 203 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 GLU 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 165 PHE Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 247 LEU 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 C residue 377 THR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 93 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 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 = 0.4697 r_free = 0.4697 target = 0.219943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.190727 restraints weight = 18704.744| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 2.52 r_work: 0.4278 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12484 Z= 0.136 Angle : 0.619 9.808 16892 Z= 0.301 Chirality : 0.042 0.183 1824 Planarity : 0.004 0.046 2144 Dihedral : 11.985 145.713 2128 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.09 % Allowed : 19.22 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1540 helix: 0.55 (0.18), residues: 836 sheet: -1.02 (0.40), residues: 148 loop : -0.88 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 52 HIS 0.008 0.001 HIS C 100 PHE 0.020 0.001 PHE B 364 TYR 0.015 0.001 TYR A 310 ARG 0.004 0.000 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 652) hydrogen bonds : angle 4.47776 ( 1875) covalent geometry : bond 0.00313 (12484) covalent geometry : angle 0.61880 (16892) *********************** 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 224 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7446 (tpt) cc_final: 0.7176 (tpt) REVERT: A 211 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7794 (pp) REVERT: B 63 ILE cc_start: 0.5814 (OUTLIER) cc_final: 0.5295 (mt) REVERT: B 81 LEU cc_start: 0.7756 (pp) cc_final: 0.7251 (tp) REVERT: B 300 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6053 (ptt) REVERT: C 86 ILE cc_start: 0.8389 (mm) cc_final: 0.8170 (mt) REVERT: D 135 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.6044 (ptm) REVERT: D 202 MET cc_start: 0.3225 (tmm) cc_final: 0.2876 (tmm) outliers start: 38 outliers final: 22 residues processed: 210 average time/residue: 0.2108 time to fit residues: 67.4632 Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 GLU 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 165 PHE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 GLN 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 377 THR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 135 MET 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 74 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** 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 = 0.4651 r_free = 0.4651 target = 0.214061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.183697 restraints weight = 18661.493| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.53 r_work: 0.4203 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12484 Z= 0.251 Angle : 0.750 10.472 16892 Z= 0.368 Chirality : 0.047 0.200 1824 Planarity : 0.005 0.048 2144 Dihedral : 12.361 156.398 2128 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.75 % Allowed : 18.89 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1540 helix: 0.23 (0.18), residues: 832 sheet: -1.07 (0.40), residues: 148 loop : -0.89 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 52 HIS 0.008 0.001 HIS A 157 PHE 0.016 0.002 PHE B 389 TYR 0.024 0.002 TYR B 301 ARG 0.008 0.001 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 652) hydrogen bonds : angle 4.85422 ( 1875) covalent geometry : bond 0.00585 (12484) covalent geometry : angle 0.75011 (16892) *********************** 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 218 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8000 (pp) REVERT: B 63 ILE cc_start: 0.5641 (OUTLIER) cc_final: 0.5113 (mt) REVERT: B 300 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6119 (ptt) REVERT: C 86 ILE cc_start: 0.8549 (mm) cc_final: 0.8338 (mt) REVERT: D 135 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.6046 (ptm) REVERT: D 369 LYS cc_start: 0.5056 (tmtt) cc_final: 0.4133 (tppt) outliers start: 46 outliers final: 28 residues processed: 204 average time/residue: 0.2114 time to fit residues: 65.8856 Evaluate side-chains 188 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 247 LEU 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 C residue 377 THR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 205 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 94 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 42 optimal weight: 0.0670 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 0.0030 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 overall best weight: 0.5930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 322 HIS ** 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 = 0.4658 r_free = 0.4658 target = 0.216471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.192584 restraints weight = 18838.702| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.08 r_work: 0.4252 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12484 Z= 0.122 Angle : 0.625 10.911 16892 Z= 0.305 Chirality : 0.042 0.189 1824 Planarity : 0.004 0.049 2144 Dihedral : 11.951 150.946 2128 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.04 % Allowed : 20.77 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1540 helix: 0.59 (0.18), residues: 836 sheet: -0.93 (0.41), residues: 148 loop : -0.98 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 52 HIS 0.006 0.001 HIS B 278 PHE 0.015 0.001 PHE B 364 TYR 0.023 0.001 TYR D 97 ARG 0.003 0.000 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 652) hydrogen bonds : angle 4.44056 ( 1875) covalent geometry : bond 0.00271 (12484) covalent geometry : angle 0.62485 (16892) *********************** 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 200 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.7305 (mt) cc_final: 0.6980 (mt) REVERT: A 211 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7842 (pp) REVERT: B 63 ILE cc_start: 0.5717 (OUTLIER) cc_final: 0.5070 (mt) REVERT: B 300 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6105 (ptt) REVERT: C 86 ILE cc_start: 0.8373 (mm) cc_final: 0.8125 (mt) REVERT: C 345 ASP cc_start: 0.6519 (m-30) cc_final: 0.6285 (m-30) REVERT: D 202 MET cc_start: 0.3242 (tmm) cc_final: 0.2950 (tmm) outliers start: 25 outliers final: 17 residues processed: 191 average time/residue: 0.2138 time to fit residues: 62.9858 Evaluate side-chains 181 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 211 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 63 ILE Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 323 CYS 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 12 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.210526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.187097 restraints weight = 18576.054| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 1.96 r_work: 0.4206 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12484 Z= 0.187 Angle : 0.681 11.442 16892 Z= 0.334 Chirality : 0.044 0.250 1824 Planarity : 0.004 0.053 2144 Dihedral : 12.038 157.664 2128 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.28 % Allowed : 20.68 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1540 helix: 0.49 (0.18), residues: 832 sheet: -0.89 (0.42), residues: 148 loop : -0.83 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 52 HIS 0.008 0.001 HIS B 79 PHE 0.014 0.002 PHE B 226 TYR 0.041 0.002 TYR A 310 ARG 0.004 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 652) hydrogen bonds : angle 4.64091 ( 1875) covalent geometry : bond 0.00444 (12484) covalent geometry : angle 0.68103 (16892) *********************** 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 188 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.6414 (mpp) cc_final: 0.4978 (ptp) REVERT: A 211 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7952 (pp) REVERT: B 63 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5148 (mt) REVERT: B 300 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6049 (ptt) REVERT: C 86 ILE cc_start: 0.8474 (mm) cc_final: 0.8234 (mt) REVERT: C 258 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7077 (mt) outliers start: 28 outliers final: 22 residues processed: 180 average time/residue: 0.2049 time to fit residues: 57.2400 Evaluate side-chains 179 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 273 THR 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 165 PHE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain C residue 258 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 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 323 CYS 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 87 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 137 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.211334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.183559 restraints weight = 18758.895| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.48 r_work: 0.4199 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12484 Z= 0.120 Angle : 0.626 12.319 16892 Z= 0.305 Chirality : 0.042 0.220 1824 Planarity : 0.004 0.048 2144 Dihedral : 11.783 154.422 2128 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.87 % Allowed : 21.42 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1540 helix: 0.70 (0.18), residues: 832 sheet: -0.86 (0.44), residues: 140 loop : -0.82 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 52 HIS 0.007 0.001 HIS B 79 PHE 0.015 0.001 PHE B 364 TYR 0.031 0.001 TYR A 310 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 652) hydrogen bonds : angle 4.42761 ( 1875) covalent geometry : bond 0.00271 (12484) covalent geometry : angle 0.62603 (16892) ********************** 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 191 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7348 (tpt) cc_final: 0.7108 (tpt) REVERT: A 202 MET cc_start: 0.6188 (mpp) cc_final: 0.4922 (ptp) REVERT: A 211 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7805 (pp) REVERT: B 63 ILE cc_start: 0.5798 (OUTLIER) cc_final: 0.5286 (mt) REVERT: B 81 LEU cc_start: 0.7869 (pp) cc_final: 0.7200 (tp) REVERT: B 300 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6162 (ptt) REVERT: C 86 ILE cc_start: 0.8447 (mm) cc_final: 0.8185 (mt) REVERT: C 256 LEU cc_start: 0.7234 (tp) cc_final: 0.7029 (tt) REVERT: C 285 GLN cc_start: 0.5625 (pt0) cc_final: 0.4632 (mt0) REVERT: D 135 MET cc_start: 0.6065 (tmm) cc_final: 0.5802 (ptm) REVERT: D 202 MET cc_start: 0.3084 (tmm) cc_final: 0.2771 (tmm) outliers start: 23 outliers final: 19 residues processed: 183 average time/residue: 0.2127 time to fit residues: 59.9029 Evaluate side-chains 181 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 273 THR 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 165 PHE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 323 CYS 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 115 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 138 optimal weight: 0.0010 chunk 8 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.210342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.182219 restraints weight = 18760.771| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 2.47 r_work: 0.4190 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12484 Z= 0.135 Angle : 0.647 12.449 16892 Z= 0.314 Chirality : 0.043 0.225 1824 Planarity : 0.004 0.048 2144 Dihedral : 11.699 156.861 2128 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.20 % Allowed : 20.77 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1540 helix: 0.70 (0.18), residues: 832 sheet: -0.82 (0.44), residues: 140 loop : -0.79 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 52 HIS 0.007 0.001 HIS B 79 PHE 0.026 0.001 PHE B 364 TYR 0.030 0.001 TYR A 310 ARG 0.003 0.000 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 652) hydrogen bonds : angle 4.44702 ( 1875) covalent geometry : bond 0.00316 (12484) covalent geometry : angle 0.64713 (16892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5557.11 seconds wall clock time: 98 minutes 56.83 seconds (5936.83 seconds total)