Starting phenix.real_space_refine on Wed Sep 17 23:42:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jq4_61722/09_2025/9jq4_61722_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jq4_61722/09_2025/9jq4_61722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jq4_61722/09_2025/9jq4_61722_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jq4_61722/09_2025/9jq4_61722_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jq4_61722/09_2025/9jq4_61722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jq4_61722/09_2025/9jq4_61722.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.100 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 7672 2.51 5 N 2136 2.21 5 O 2328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12248 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: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCO': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCO': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCO': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCO': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.22, per 1000 atoms: 0.26 Number of scatterers: 12248 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 7672 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 525.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 14 sheets defined 59.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 removed outlier: 3.944A pdb=" N ASN A 11 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 32 removed outlier: 4.043A pdb=" N GLU A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.704A pdb=" N TYR A 69 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 70 " --> pdb=" O VAL A 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 70' Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.724A pdb=" N HIS A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 3.550A pdb=" N SER A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.525A pdb=" N GLU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 242 through 258 removed outlier: 3.533A pdb=" N LEU A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.680A pdb=" N LEU A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Proline residue: A 275 - end of helix removed outlier: 3.617A pdb=" N HIS A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 321 removed outlier: 3.565A pdb=" N LYS A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 350 removed outlier: 3.641A pdb=" N CYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 332 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.689A pdb=" N ILE A 356 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 369 removed outlier: 3.502A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.651A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 391 removed outlier: 3.736A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.953A pdb=" N ASN B 11 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 47 through 58 removed outlier: 3.518A pdb=" N PHE B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.760A pdb=" N HIS B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.507A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.567A pdb=" N LYS B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Proline residue: B 122 - end of helix removed outlier: 4.051A pdb=" N SER B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 removed outlier: 3.589A pdb=" N MET B 147 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 243 through 258 removed outlier: 4.056A pdb=" N SER B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 280 removed outlier: 3.846A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Proline residue: B 275 - end of helix Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.576A pdb=" N GLU B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 351 removed outlier: 3.742A pdb=" N ILE B 332 " --> pdb=" O CYS B 328 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.704A pdb=" N ILE B 356 " --> pdb=" O ASN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 369 removed outlier: 3.724A pdb=" N LEU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 373 Processing helix chain 'B' and resid 377 through 391 removed outlier: 3.786A pdb=" N PHE B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.708A pdb=" N ASN C 11 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 32 removed outlier: 3.546A pdb=" N GLU C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 75 through 90 removed outlier: 3.659A pdb=" N ALA C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.726A pdb=" N ARG C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 143 through 147 Processing helix chain 'C' and resid 243 through 258 removed outlier: 3.697A pdb=" N ARG C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 277 Proline residue: C 275 - end of helix Processing helix chain 'C' and resid 290 through 319 Processing helix chain 'C' and resid 324 through 351 removed outlier: 3.712A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 369 removed outlier: 3.720A pdb=" N LEU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 366 " --> pdb=" O GLY C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 373 Processing helix chain 'C' and resid 377 through 388 Processing helix chain 'D' and resid 8 through 12 removed outlier: 3.899A pdb=" N ASN D 11 " --> pdb=" O ASP D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 29 removed outlier: 3.601A pdb=" N GLN D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 35 through 43 Processing helix chain 'D' and resid 47 through 59 Processing helix chain 'D' and resid 75 through 86 removed outlier: 3.537A pdb=" N HIS D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 102 removed outlier: 3.610A pdb=" N GLY D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 143 through 147 removed outlier: 3.977A pdb=" N MET D 147 " --> pdb=" O VAL D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 191 Processing helix chain 'D' and resid 242 through 258 removed outlier: 4.358A pdb=" N VAL D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP D 252 " --> pdb=" O MET D 248 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 278 removed outlier: 3.781A pdb=" N LEU D 263 " --> pdb=" O ALA D 259 " (cutoff:3.500A) Proline residue: D 275 - end of helix removed outlier: 3.505A pdb=" N HIS D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 319 Processing helix chain 'D' and resid 324 through 351 removed outlier: 3.666A pdb=" N ILE D 332 " --> pdb=" O CYS D 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 369 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.739A pdb=" N ILE D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 392 removed outlier: 3.993A pdb=" N ASP D 392 " --> pdb=" O ALA D 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 4.286A pdb=" N ALA A 195 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 153 removed outlier: 5.971A pdb=" N TYR A 158 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A 230 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU A 160 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 228 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 162 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP A 166 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS A 222 " --> pdb=" O TRP A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.582A pdb=" N ALA B 132 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 179 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA B 195 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.950A pdb=" N LYS B 150 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 168 removed outlier: 4.324A pdb=" N TRP B 166 " --> pdb=" O CYS B 222 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N CYS B 222 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 134 removed outlier: 6.532A pdb=" N ALA C 132 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR C 179 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA C 134 " --> pdb=" O TYR C 179 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N LYS C 181 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA C 195 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 150 through 154 removed outlier: 3.602A pdb=" N LYS C 150 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 152 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR C 158 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS C 230 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU C 160 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TRP C 166 " --> pdb=" O CYS C 222 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS C 222 " --> pdb=" O TRP C 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AB2, first strand: chain 'D' and resid 131 through 134 removed outlier: 4.030A pdb=" N ALA D 195 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 150 through 153 removed outlier: 3.525A pdb=" N GLU D 152 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY D 162 " --> pdb=" O PHE D 226 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP D 166 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS D 222 " --> pdb=" O TRP D 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 150 through 153 removed outlier: 3.525A pdb=" N GLU D 152 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 281 through 282 655 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.31: 2053 1.31 - 1.47: 4873 1.47 - 1.64: 5389 1.64 - 1.80: 73 1.80 - 1.96: 92 Bond restraints: 12480 Sorted by residual: bond pdb=" C1 BCO A 401 " pdb=" C2 BCO A 401 " ideal model delta sigma weight residual 1.549 1.253 0.296 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C1 BCO B 401 " pdb=" C2 BCO B 401 " ideal model delta sigma weight residual 1.549 1.259 0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C1 BCO D 401 " pdb=" C2 BCO D 401 " ideal model delta sigma weight residual 1.549 1.263 0.286 2.00e-02 2.50e+03 2.04e+02 bond pdb=" C1 BCO C 401 " pdb=" C2 BCO C 401 " ideal model delta sigma weight residual 1.549 1.263 0.286 2.00e-02 2.50e+03 2.04e+02 bond pdb=" C22 BCO D 401 " pdb=" S1 BCO D 401 " ideal model delta sigma weight residual 1.782 1.964 -0.182 2.00e-02 2.50e+03 8.25e+01 ... (remaining 12475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 16681 5.02 - 10.04: 172 10.04 - 15.06: 26 15.06 - 20.08: 2 20.08 - 25.10: 3 Bond angle restraints: 16884 Sorted by residual: angle pdb=" C21 BCO D 401 " pdb=" S1 BCO D 401 " pdb=" C22 BCO D 401 " ideal model delta sigma weight residual 100.75 125.85 -25.10 3.00e+00 1.11e-01 7.00e+01 angle pdb=" C23 BCO D 401 " pdb=" C22 BCO D 401 " pdb=" O17 BCO D 401 " ideal model delta sigma weight residual 123.48 101.76 21.72 3.00e+00 1.11e-01 5.24e+01 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 BCO A 401 " pdb=" S1 BCO A 401 " pdb=" C22 BCO A 401 " ideal model delta sigma weight residual 100.75 121.13 -20.38 3.00e+00 1.11e-01 4.61e+01 angle pdb=" C23 BCO D 401 " pdb=" C22 BCO D 401 " pdb=" S1 BCO D 401 " ideal model delta sigma weight residual 113.49 129.98 -16.49 3.00e+00 1.11e-01 3.02e+01 ... (remaining 16879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.48: 7371 28.48 - 56.97: 253 56.97 - 85.45: 38 85.45 - 113.93: 4 113.93 - 142.42: 2 Dihedral angle restraints: 7668 sinusoidal: 3304 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=" C7 BCO C 401 " pdb=" C4 BCO C 401 " pdb=" N1 BCO C 401 " pdb=" O1 BCO C 401 " ideal model delta sinusoidal sigma weight residual 280.07 137.65 142.42 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C6 BCO C 401 " pdb=" C4 BCO C 401 " pdb=" N1 BCO C 401 " pdb=" O1 BCO C 401 " ideal model delta sinusoidal sigma weight residual 93.64 -41.63 135.27 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 7665 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: 1.80 - 2.42: 43 2.42 - 3.04: 7223 3.04 - 3.66: 18705 3.66 - 4.28: 29270 4.28 - 4.90: 48975 Nonbonded interactions: 104216 Sorted by model distance: nonbonded pdb=" O GLY B 374 " pdb=" O17 BCO B 401 " model vdw 1.802 3.040 nonbonded pdb=" O SER C 142 " pdb=" O15 BCO C 401 " model vdw 2.056 3.040 nonbonded pdb=" OE1 GLU D 84 " pdb=" OH TYR D 312 " model vdw 2.221 3.040 nonbonded pdb=" O2 BCO A 401 " pdb=" O3 BCO A 401 " model vdw 2.244 2.432 nonbonded pdb=" OH TYR C 355 " pdb=" O ARG D 366 " model vdw 2.262 3.040 ... (remaining 104211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 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 : 0.011 0.502 12481 Z= 0.689 Angle : 1.127 25.095 16884 Z= 0.465 Chirality : 0.056 1.413 1824 Planarity : 0.004 0.063 2144 Dihedral : 13.575 142.418 4908 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.17 % Favored : 98.77 % Rotamer: Outliers : 1.38 % Allowed : 4.40 % Favored : 94.22 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.18), residues: 1540 helix: -0.75 (0.17), residues: 784 sheet: -1.15 (0.40), residues: 128 loop : -1.50 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 255 TYR 0.021 0.001 TYR C 245 PHE 0.006 0.000 PHE A 51 TRP 0.004 0.001 TRP B 52 HIS 0.002 0.000 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.01021 (12480) covalent geometry : angle 1.12665 (16884) hydrogen bonds : bond 0.21503 ( 652) hydrogen bonds : angle 6.66064 ( 1875) Misc. bond : bond 0.50197 ( 1) *********************** 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 377 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 360 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.8005 (mmt) cc_final: 0.7682 (mmt) REVERT: B 24 MET cc_start: 0.6342 (mmp) cc_final: 0.6037 (mmm) outliers start: 17 outliers final: 3 residues processed: 373 average time/residue: 0.5744 time to fit residues: 231.6666 Evaluate side-chains 170 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 135 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 31 HIS A 68 GLN A 111 ASN A 161 ASN A 294 GLN A 341 GLN B 31 HIS B 68 GLN B 116 GLN B 156 ASN B 163 ASN B 278 HIS B 289 HIS B 309 GLN B 341 GLN C 11 ASN C 19 GLN C 54 GLN C 57 ASN C 111 ASN C 241 ASN C 289 HIS C 341 GLN C 348 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 68 GLN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 139 ASN D 163 ASN D 220 ASN D 291 GLN D 341 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.202270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178268 restraints weight = 15942.598| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.27 r_work: 0.3924 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12481 Z= 0.132 Angle : 0.631 8.434 16884 Z= 0.299 Chirality : 0.042 0.196 1824 Planarity : 0.004 0.035 2144 Dihedral : 14.708 178.020 2131 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.58 % Allowed : 16.61 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1540 helix: 0.35 (0.17), residues: 828 sheet: -1.15 (0.38), residues: 128 loop : -1.21 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 88 TYR 0.014 0.001 TYR D 129 PHE 0.014 0.001 PHE C 290 TRP 0.015 0.002 TRP A 166 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00287 (12480) covalent geometry : angle 0.63119 (16884) hydrogen bonds : bond 0.04345 ( 652) hydrogen bonds : angle 4.75386 ( 1875) Misc. bond : bond 0.00041 ( 1) *********************** 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 236 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.6372 (OUTLIER) cc_final: 0.5975 (mp10) REVERT: A 46 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7750 (mttt) REVERT: A 297 MET cc_start: 0.6887 (mtm) cc_final: 0.6682 (mtp) REVERT: B 22 GLN cc_start: 0.6295 (mm-40) cc_final: 0.5731 (pt0) REVERT: B 183 ASP cc_start: 0.7662 (t0) cc_final: 0.7412 (t0) REVERT: B 320 GLU cc_start: 0.6506 (mm-30) cc_final: 0.6127 (mm-30) REVERT: C 121 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6789 (mp) REVERT: C 252 ASP cc_start: 0.7303 (m-30) cc_final: 0.7066 (m-30) outliers start: 44 outliers final: 12 residues processed: 224 average time/residue: 0.5268 time to fit residues: 128.9224 Evaluate side-chains 169 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 246 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 111 ASN A 313 ASN B 169 ASN B 272 HIS B 278 HIS B 309 GLN C 106 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 ASN D 43 ASN D 107 GLN D 111 ASN D 220 ASN D 309 GLN D 313 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.198685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.174331 restraints weight = 16074.178| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.27 r_work: 0.3885 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12481 Z= 0.118 Angle : 0.576 7.960 16884 Z= 0.274 Chirality : 0.041 0.166 1824 Planarity : 0.004 0.053 2144 Dihedral : 13.657 141.478 2125 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.09 % Allowed : 17.83 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.20), residues: 1540 helix: 1.02 (0.18), residues: 808 sheet: -1.04 (0.38), residues: 128 loop : -1.00 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 41 TYR 0.013 0.001 TYR C 158 PHE 0.021 0.001 PHE D 205 TRP 0.015 0.001 TRP A 166 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00266 (12480) covalent geometry : angle 0.57583 (16884) hydrogen bonds : bond 0.03874 ( 652) hydrogen bonds : angle 4.42072 ( 1875) Misc. bond : bond 0.00086 ( 1) *********************** 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 203 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6588 (tpt90) REVERT: A 22 GLN cc_start: 0.6224 (OUTLIER) cc_final: 0.5878 (mp10) REVERT: A 37 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6718 (tp-100) REVERT: A 46 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7774 (mttt) REVERT: A 150 LYS cc_start: 0.7840 (ptpp) cc_final: 0.7286 (tttm) REVERT: A 242 LYS cc_start: 0.7674 (mptt) cc_final: 0.7442 (mmpt) REVERT: A 312 TYR cc_start: 0.6384 (m-80) cc_final: 0.6175 (m-80) REVERT: A 379 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7078 (mm-30) REVERT: B 22 GLN cc_start: 0.6289 (mm-40) cc_final: 0.5703 (pt0) REVERT: B 24 MET cc_start: 0.6934 (mmm) cc_final: 0.6363 (mmm) REVERT: B 63 ILE cc_start: 0.6517 (OUTLIER) cc_final: 0.6268 (tt) REVERT: B 114 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6038 (pt0) REVERT: B 183 ASP cc_start: 0.7795 (t0) cc_final: 0.7366 (t0) REVERT: B 320 GLU cc_start: 0.6477 (mm-30) cc_final: 0.6190 (mp0) REVERT: C 18 ARG cc_start: 0.4874 (mtt-85) cc_final: 0.4521 (mtm180) REVERT: C 137 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: C 318 CYS cc_start: 0.7658 (m) cc_final: 0.7295 (t) REVERT: D 107 GLN cc_start: 0.5009 (OUTLIER) cc_final: 0.4658 (tp40) REVERT: D 387 ARG cc_start: 0.6735 (mtt-85) cc_final: 0.6335 (mtt90) outliers start: 38 outliers final: 9 residues processed: 193 average time/residue: 0.5274 time to fit residues: 110.8876 Evaluate side-chains 169 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 160 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 5 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN B 113 ASN B 278 HIS B 357 ASN C 348 GLN D 107 GLN D 111 ASN D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.198036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.174350 restraints weight = 15915.177| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.22 r_work: 0.3882 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12481 Z= 0.109 Angle : 0.559 8.311 16884 Z= 0.265 Chirality : 0.040 0.259 1824 Planarity : 0.003 0.046 2144 Dihedral : 13.171 136.501 2125 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.93 % Allowed : 18.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.21), residues: 1540 helix: 1.29 (0.18), residues: 808 sheet: -0.93 (0.39), residues: 128 loop : -0.93 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 21 TYR 0.013 0.001 TYR C 355 PHE 0.021 0.001 PHE D 205 TRP 0.014 0.001 TRP A 166 HIS 0.003 0.000 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00243 (12480) covalent geometry : angle 0.55878 (16884) hydrogen bonds : bond 0.03611 ( 652) hydrogen bonds : angle 4.27551 ( 1875) Misc. bond : bond 0.00001 ( 1) *********************** 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 193 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6671 (tpt90) REVERT: A 22 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5981 (mp10) REVERT: A 37 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.6650 (tp40) REVERT: A 46 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7751 (mttt) REVERT: A 49 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6677 (mtt90) REVERT: A 150 LYS cc_start: 0.7869 (ptpp) cc_final: 0.7331 (tttm) REVERT: A 196 PHE cc_start: 0.7190 (m-80) cc_final: 0.6792 (m-80) REVERT: A 242 LYS cc_start: 0.7582 (mptt) cc_final: 0.7206 (mmpt) REVERT: B 22 GLN cc_start: 0.6285 (mm-40) cc_final: 0.5667 (pt0) REVERT: B 63 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.6297 (tt) REVERT: B 114 GLU cc_start: 0.6735 (pp20) cc_final: 0.6059 (pt0) REVERT: B 183 ASP cc_start: 0.7873 (t0) cc_final: 0.7588 (t0) REVERT: B 320 GLU cc_start: 0.6394 (mm-30) cc_final: 0.6149 (mp0) REVERT: C 18 ARG cc_start: 0.4998 (mtt-85) cc_final: 0.4684 (mtm180) REVERT: C 121 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6769 (mp) REVERT: C 137 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: C 318 CYS cc_start: 0.7629 (m) cc_final: 0.7311 (t) REVERT: D 313 ASN cc_start: 0.6656 (m-40) cc_final: 0.6383 (m110) REVERT: D 387 ARG cc_start: 0.6836 (mtt-85) cc_final: 0.6559 (mtt90) outliers start: 36 outliers final: 15 residues processed: 186 average time/residue: 0.5608 time to fit residues: 113.2908 Evaluate side-chains 172 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 143 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 278 HIS D 139 ASN D 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.197735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.173764 restraints weight = 16141.588| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.26 r_work: 0.3872 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12481 Z= 0.107 Angle : 0.544 9.492 16884 Z= 0.260 Chirality : 0.039 0.154 1824 Planarity : 0.003 0.037 2144 Dihedral : 12.446 132.865 2125 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.18 % Allowed : 18.49 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.21), residues: 1540 helix: 1.39 (0.18), residues: 824 sheet: -0.93 (0.41), residues: 116 loop : -0.88 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.011 0.001 TYR A 97 PHE 0.022 0.001 PHE D 205 TRP 0.014 0.001 TRP A 166 HIS 0.003 0.000 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00243 (12480) covalent geometry : angle 0.54396 (16884) hydrogen bonds : bond 0.03493 ( 652) hydrogen bonds : angle 4.16814 ( 1875) Misc. bond : bond 0.00033 ( 1) *********************** 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 200 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6691 (tpt90) REVERT: A 22 GLN cc_start: 0.6125 (OUTLIER) cc_final: 0.5845 (mp10) REVERT: A 150 LYS cc_start: 0.7840 (ptpp) cc_final: 0.7330 (tttm) REVERT: A 196 PHE cc_start: 0.7267 (m-80) cc_final: 0.6874 (m-80) REVERT: A 242 LYS cc_start: 0.7483 (mptt) cc_final: 0.7088 (mmpt) REVERT: A 358 ASP cc_start: 0.7969 (m-30) cc_final: 0.7388 (t0) REVERT: A 379 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: B 16 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6788 (mp0) REVERT: B 24 MET cc_start: 0.6970 (mmm) cc_final: 0.6629 (mmm) REVERT: B 41 ARG cc_start: 0.6936 (ttp80) cc_final: 0.6543 (ttp80) REVERT: B 63 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6240 (tt) REVERT: B 114 GLU cc_start: 0.6838 (pp20) cc_final: 0.6148 (pt0) REVERT: B 157 HIS cc_start: 0.5886 (m170) cc_final: 0.5637 (m-70) REVERT: B 183 ASP cc_start: 0.7914 (t0) cc_final: 0.7608 (t0) REVERT: B 320 GLU cc_start: 0.6349 (mm-30) cc_final: 0.6115 (mp0) REVERT: C 121 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6891 (mp) REVERT: C 137 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: C 318 CYS cc_start: 0.7572 (m) cc_final: 0.7270 (t) REVERT: D 313 ASN cc_start: 0.6656 (m-40) cc_final: 0.6387 (m110) REVERT: D 387 ARG cc_start: 0.6830 (mtt-85) cc_final: 0.6561 (mtt90) outliers start: 39 outliers final: 13 residues processed: 191 average time/residue: 0.5433 time to fit residues: 112.6575 Evaluate side-chains 166 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 313 ASN A 348 GLN B 107 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 278 HIS D 11 ASN D 220 ASN D 309 GLN D 313 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.196758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.172545 restraints weight = 16116.581| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.25 r_work: 0.3864 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12481 Z= 0.113 Angle : 0.561 9.989 16884 Z= 0.267 Chirality : 0.040 0.225 1824 Planarity : 0.004 0.057 2144 Dihedral : 11.755 129.078 2125 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.52 % Allowed : 19.54 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.21), residues: 1540 helix: 1.46 (0.18), residues: 828 sheet: -0.96 (0.41), residues: 116 loop : -0.66 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 18 TYR 0.020 0.001 TYR D 245 PHE 0.020 0.001 PHE D 205 TRP 0.014 0.001 TRP A 166 HIS 0.003 0.000 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00261 (12480) covalent geometry : angle 0.56121 (16884) hydrogen bonds : bond 0.03578 ( 652) hydrogen bonds : angle 4.15401 ( 1875) Misc. bond : bond 0.00009 ( 1) *********************** 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 187 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6769 (tpt90) REVERT: A 22 GLN cc_start: 0.6148 (OUTLIER) cc_final: 0.5875 (mp10) REVERT: A 150 LYS cc_start: 0.7974 (ptpp) cc_final: 0.7527 (tttm) REVERT: A 196 PHE cc_start: 0.7307 (m-80) cc_final: 0.6939 (m-80) REVERT: A 379 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: B 16 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6825 (mp0) REVERT: B 24 MET cc_start: 0.7034 (mmm) cc_final: 0.6799 (mmm) REVERT: B 63 ILE cc_start: 0.6517 (OUTLIER) cc_final: 0.6266 (tt) REVERT: B 114 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6155 (pt0) REVERT: B 157 HIS cc_start: 0.6112 (m170) cc_final: 0.5895 (m-70) REVERT: B 183 ASP cc_start: 0.7906 (t0) cc_final: 0.7606 (t0) REVERT: C 121 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6916 (mp) REVERT: C 137 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7638 (tp30) REVERT: C 318 CYS cc_start: 0.7505 (m) cc_final: 0.7234 (t) REVERT: D 135 MET cc_start: 0.6079 (ptt) cc_final: 0.5696 (ttp) REVERT: D 313 ASN cc_start: 0.6577 (m110) cc_final: 0.6338 (m110) REVERT: D 387 ARG cc_start: 0.6799 (mtt-85) cc_final: 0.6502 (mtt90) outliers start: 31 outliers final: 13 residues processed: 179 average time/residue: 0.5210 time to fit residues: 101.8423 Evaluate side-chains 160 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 113 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS D 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.192767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.168008 restraints weight = 16221.893| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.28 r_work: 0.3806 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12481 Z= 0.138 Angle : 0.601 11.049 16884 Z= 0.286 Chirality : 0.041 0.248 1824 Planarity : 0.004 0.050 2144 Dihedral : 11.583 124.229 2125 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.52 % Allowed : 21.34 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.21), residues: 1540 helix: 1.40 (0.18), residues: 820 sheet: -0.83 (0.43), residues: 116 loop : -0.58 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 41 TYR 0.012 0.001 TYR D 310 PHE 0.018 0.001 PHE D 205 TRP 0.017 0.002 TRP A 166 HIS 0.008 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00322 (12480) covalent geometry : angle 0.60115 (16884) hydrogen bonds : bond 0.03953 ( 652) hydrogen bonds : angle 4.23509 ( 1875) Misc. bond : bond 0.00042 ( 1) *********************** 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 190 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6663 (tpt90) REVERT: A 22 GLN cc_start: 0.6157 (OUTLIER) cc_final: 0.5829 (mp10) REVERT: A 150 LYS cc_start: 0.8011 (ptpp) cc_final: 0.7614 (tttm) REVERT: A 196 PHE cc_start: 0.7348 (m-80) cc_final: 0.6975 (m-80) REVERT: A 358 ASP cc_start: 0.7894 (m-30) cc_final: 0.7324 (t0) REVERT: A 379 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: B 16 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6751 (mp0) REVERT: B 63 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6271 (tt) REVERT: B 157 HIS cc_start: 0.6116 (m170) cc_final: 0.5873 (m-70) REVERT: C 22 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6403 (tt0) REVERT: C 318 CYS cc_start: 0.7529 (m) cc_final: 0.7219 (t) REVERT: D 135 MET cc_start: 0.6427 (ptt) cc_final: 0.6168 (ttp) REVERT: D 313 ASN cc_start: 0.6588 (m110) cc_final: 0.6253 (m110) REVERT: D 387 ARG cc_start: 0.6731 (mtt-85) cc_final: 0.6301 (mtt90) outliers start: 31 outliers final: 15 residues processed: 182 average time/residue: 0.4987 time to fit residues: 99.2715 Evaluate side-chains 164 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 14 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 92 optimal weight: 0.1980 chunk 127 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN B 157 HIS B 169 ASN ** B 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.195223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.170919 restraints weight = 16246.205| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.27 r_work: 0.3838 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12481 Z= 0.107 Angle : 0.564 11.614 16884 Z= 0.269 Chirality : 0.039 0.147 1824 Planarity : 0.003 0.054 2144 Dihedral : 11.262 119.486 2125 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.61 % Allowed : 21.99 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.21), residues: 1540 helix: 1.51 (0.18), residues: 828 sheet: -0.82 (0.43), residues: 116 loop : -0.66 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 41 TYR 0.016 0.001 TYR D 310 PHE 0.018 0.001 PHE D 205 TRP 0.014 0.001 TRP A 166 HIS 0.005 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00243 (12480) covalent geometry : angle 0.56357 (16884) hydrogen bonds : bond 0.03472 ( 652) hydrogen bonds : angle 4.14211 ( 1875) Misc. bond : bond 0.00005 ( 1) *********************** 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 194 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6734 (ttt-90) REVERT: A 22 GLN cc_start: 0.6144 (OUTLIER) cc_final: 0.5804 (mp10) REVERT: A 150 LYS cc_start: 0.7999 (ptpp) cc_final: 0.7646 (tttm) REVERT: A 191 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8128 (mmt90) REVERT: A 196 PHE cc_start: 0.7366 (m-80) cc_final: 0.7028 (m-80) REVERT: A 358 ASP cc_start: 0.7893 (m-30) cc_final: 0.7328 (t0) REVERT: A 379 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: B 16 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6772 (mp0) REVERT: B 63 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6253 (tt) REVERT: B 114 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6110 (pt0) REVERT: C 24 MET cc_start: 0.7687 (mmm) cc_final: 0.7450 (mmp) REVERT: C 137 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7630 (tp30) REVERT: D 37 GLN cc_start: 0.5079 (tp40) cc_final: 0.4710 (mt0) REVERT: D 135 MET cc_start: 0.6372 (ptt) cc_final: 0.6144 (ttp) REVERT: D 272 HIS cc_start: 0.6873 (m170) cc_final: 0.6453 (m170) REVERT: D 305 MET cc_start: 0.8605 (mmp) cc_final: 0.8360 (mmt) REVERT: D 313 ASN cc_start: 0.6498 (m110) cc_final: 0.6217 (m110) REVERT: D 387 ARG cc_start: 0.6728 (mtt-85) cc_final: 0.6347 (mtt90) outliers start: 32 outliers final: 10 residues processed: 185 average time/residue: 0.5263 time to fit residues: 106.2970 Evaluate side-chains 165 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.194833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.170636 restraints weight = 16200.950| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.26 r_work: 0.3838 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12481 Z= 0.114 Angle : 0.576 12.045 16884 Z= 0.276 Chirality : 0.040 0.152 1824 Planarity : 0.004 0.053 2144 Dihedral : 11.124 115.753 2125 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.95 % Allowed : 23.45 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.21), residues: 1540 helix: 1.48 (0.18), residues: 828 sheet: -0.88 (0.40), residues: 140 loop : -0.74 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 41 TYR 0.012 0.001 TYR C 355 PHE 0.019 0.001 PHE C 290 TRP 0.013 0.001 TRP A 166 HIS 0.006 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00262 (12480) covalent geometry : angle 0.57637 (16884) hydrogen bonds : bond 0.03526 ( 652) hydrogen bonds : angle 4.13398 ( 1875) Misc. bond : bond 0.00000 ( 1) *********************** 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 181 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6770 (ttt-90) REVERT: A 22 GLN cc_start: 0.6157 (OUTLIER) cc_final: 0.5814 (mp10) REVERT: A 150 LYS cc_start: 0.8018 (ptpp) cc_final: 0.7696 (tttm) REVERT: A 191 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (mmt90) REVERT: A 196 PHE cc_start: 0.7405 (m-80) cc_final: 0.7061 (m-80) REVERT: A 216 MET cc_start: 0.8773 (mmp) cc_final: 0.8437 (mmt) REVERT: A 358 ASP cc_start: 0.7917 (m-30) cc_final: 0.7356 (t0) REVERT: A 379 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: B 63 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6224 (tt) REVERT: B 114 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6103 (pt0) REVERT: C 24 MET cc_start: 0.7711 (mmm) cc_final: 0.7511 (mmp) REVERT: C 137 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: D 37 GLN cc_start: 0.5114 (tp40) cc_final: 0.4760 (mt0) REVERT: D 272 HIS cc_start: 0.6890 (m170) cc_final: 0.6482 (m170) REVERT: D 305 MET cc_start: 0.8551 (mmp) cc_final: 0.8313 (mmt) REVERT: D 313 ASN cc_start: 0.6474 (m110) cc_final: 0.6169 (m110) REVERT: D 387 ARG cc_start: 0.6636 (mtt-85) cc_final: 0.6294 (mtt90) outliers start: 24 outliers final: 13 residues processed: 175 average time/residue: 0.5192 time to fit residues: 99.3456 Evaluate side-chains 166 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 0.0970 chunk 135 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN D 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.195277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170823 restraints weight = 16215.499| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.28 r_work: 0.3846 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12481 Z= 0.108 Angle : 0.570 11.525 16884 Z= 0.272 Chirality : 0.040 0.142 1824 Planarity : 0.004 0.054 2144 Dihedral : 10.980 113.668 2125 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.87 % Allowed : 23.37 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.21), residues: 1540 helix: 1.55 (0.18), residues: 828 sheet: -0.88 (0.40), residues: 140 loop : -0.71 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 41 TYR 0.021 0.001 TYR D 310 PHE 0.017 0.001 PHE D 205 TRP 0.014 0.001 TRP A 166 HIS 0.005 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00246 (12480) covalent geometry : angle 0.56967 (16884) hydrogen bonds : bond 0.03413 ( 652) hydrogen bonds : angle 4.08549 ( 1875) Misc. bond : bond 0.00037 ( 1) ********************** 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 171 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6749 (ttt-90) REVERT: A 22 GLN cc_start: 0.6151 (OUTLIER) cc_final: 0.5814 (mp10) REVERT: A 150 LYS cc_start: 0.7986 (ptpp) cc_final: 0.7675 (tttt) REVERT: A 191 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8150 (mmt90) REVERT: A 196 PHE cc_start: 0.7380 (m-80) cc_final: 0.7039 (m-80) REVERT: A 312 TYR cc_start: 0.6387 (m-80) cc_final: 0.6144 (m-80) REVERT: A 358 ASP cc_start: 0.7904 (m-30) cc_final: 0.7331 (t0) REVERT: A 379 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: B 63 ILE cc_start: 0.6536 (OUTLIER) cc_final: 0.6217 (tt) REVERT: B 114 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6093 (pt0) REVERT: D 37 GLN cc_start: 0.5096 (tp40) cc_final: 0.4730 (mt0) REVERT: D 272 HIS cc_start: 0.6861 (m170) cc_final: 0.6426 (m170) REVERT: D 305 MET cc_start: 0.8552 (mmp) cc_final: 0.8341 (mmt) REVERT: D 313 ASN cc_start: 0.6495 (m110) cc_final: 0.6200 (m110) REVERT: D 387 ARG cc_start: 0.6620 (mtt-85) cc_final: 0.6268 (mtt90) outliers start: 23 outliers final: 12 residues processed: 165 average time/residue: 0.5456 time to fit residues: 98.1815 Evaluate side-chains 160 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 0.0770 chunk 120 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.195155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.170846 restraints weight = 16012.761| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.25 r_work: 0.3850 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12481 Z= 0.109 Angle : 0.575 11.581 16884 Z= 0.275 Chirality : 0.040 0.170 1824 Planarity : 0.004 0.052 2144 Dihedral : 10.880 111.878 2125 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.95 % Allowed : 23.45 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.21), residues: 1540 helix: 1.51 (0.18), residues: 836 sheet: -0.85 (0.40), residues: 140 loop : -0.62 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 41 TYR 0.025 0.001 TYR D 310 PHE 0.017 0.001 PHE D 205 TRP 0.013 0.001 TRP A 166 HIS 0.005 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00247 (12480) covalent geometry : angle 0.57546 (16884) hydrogen bonds : bond 0.03392 ( 652) hydrogen bonds : angle 4.06641 ( 1875) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.99 seconds wall clock time: 59 minutes 17.36 seconds (3557.36 seconds total)