Starting phenix.real_space_refine on Wed Jul 30 11:09:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jq4_61722/07_2025/9jq4_61722_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jq4_61722/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jq4_61722/07_2025/9jq4_61722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jq4_61722/07_2025/9jq4_61722.map" model { file = "/net/cci-nas-00/data/ceres_data/9jq4_61722/07_2025/9jq4_61722_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jq4_61722/07_2025/9jq4_61722_trim.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.100 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.55, per 1000 atoms: 0.70 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: 3.86 Conformation dependent library (CDL) restraints added in 1.7 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 14 sheets defined 59.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 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: 4.40 Time building geometry restraints manager: 3.92 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: 0.03 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: 1.060 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.530 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:39.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.850 ------------------------------------------------------------------------------- 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 : 12.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.17 % Favored : 98.77 % Rotamer: Outliers : 1.38 % Allowed : 4.40 % Favored : 94.22 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.18), residues: 1540 helix: -0.75 (0.17), residues: 784 sheet: -1.15 (0.40), residues: 128 loop : -1.50 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 52 HIS 0.002 0.000 HIS A 100 PHE 0.006 0.000 PHE A 51 TYR 0.021 0.001 TYR C 245 ARG 0.002 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.21503 ( 652) hydrogen bonds : angle 6.66064 ( 1875) covalent geometry : bond 0.01021 (12480) covalent geometry : angle 1.12665 (16884) 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 : 1.393 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: 1.4122 time to fit residues: 570.6087 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 : 1.379 ------------------------------------------------------------------------------- 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 128 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 37 GLN 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 272 HIS 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 169 ASN C 241 ASN C 289 HIS C 294 GLN C 341 GLN C 348 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 68 GLN 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.197883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.173553 restraints weight = 15905.610| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.23 r_work: 0.3876 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12481 Z= 0.160 Angle : 0.669 9.434 16884 Z= 0.317 Chirality : 0.043 0.211 1824 Planarity : 0.004 0.037 2144 Dihedral : 14.747 176.925 2131 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.75 % Allowed : 16.78 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1540 helix: 0.27 (0.17), residues: 828 sheet: -1.14 (0.38), residues: 128 loop : -1.25 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 166 HIS 0.004 0.001 HIS A 79 PHE 0.018 0.002 PHE C 290 TYR 0.012 0.001 TYR D 334 ARG 0.004 0.001 ARG B 88 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 652) hydrogen bonds : angle 4.79635 ( 1875) covalent geometry : bond 0.00356 (12480) covalent geometry : angle 0.66854 (16884) Misc. bond : bond 0.00118 ( 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 228 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5995 (mp10) REVERT: A 37 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.6648 (tp-100) REVERT: A 46 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7763 (mttt) REVERT: B 22 GLN cc_start: 0.6281 (mm-40) cc_final: 0.5715 (pt0) REVERT: B 183 ASP cc_start: 0.7722 (t0) cc_final: 0.7476 (t0) REVERT: B 320 GLU cc_start: 0.6482 (mm-30) cc_final: 0.6119 (mm-30) REVERT: C 35 LYS cc_start: 0.7772 (ptpp) cc_final: 0.7549 (ptpt) REVERT: C 252 ASP cc_start: 0.7352 (m-30) cc_final: 0.7109 (m-30) outliers start: 46 outliers final: 11 residues processed: 214 average time/residue: 1.1667 time to fit residues: 274.2927 Evaluate side-chains 159 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 269 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 51 optimal weight: 0.1980 chunk 130 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 106 ASN B 169 ASN B 278 HIS B 309 GLN C 106 ASN C 348 GLN D 43 ASN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.193260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.168324 restraints weight = 16137.566| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.26 r_work: 0.3816 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 12481 Z= 0.154 Angle : 0.626 8.511 16884 Z= 0.299 Chirality : 0.042 0.227 1824 Planarity : 0.004 0.035 2144 Dihedral : 13.774 141.739 2125 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.75 % Allowed : 17.59 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.20), residues: 1540 helix: 0.68 (0.18), residues: 824 sheet: -1.09 (0.42), residues: 116 loop : -1.01 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 166 HIS 0.008 0.001 HIS A 79 PHE 0.015 0.002 PHE C 290 TYR 0.012 0.001 TYR C 158 ARG 0.006 0.001 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 652) hydrogen bonds : angle 4.56438 ( 1875) covalent geometry : bond 0.00360 (12480) covalent geometry : angle 0.62610 (16884) Misc. bond : bond 0.00088 ( 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 212 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6561 (tpt90) REVERT: A 22 GLN cc_start: 0.6290 (OUTLIER) cc_final: 0.5918 (mp10) REVERT: A 46 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7822 (mttt) REVERT: A 150 LYS cc_start: 0.7841 (ptpp) cc_final: 0.7293 (tttm) REVERT: A 196 PHE cc_start: 0.7331 (m-80) cc_final: 0.6884 (m-80) REVERT: A 242 LYS cc_start: 0.7681 (mptt) cc_final: 0.7411 (mmpt) REVERT: A 358 ASP cc_start: 0.7981 (m-30) cc_final: 0.7419 (t0) REVERT: A 379 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: B 22 GLN cc_start: 0.6351 (mm-40) cc_final: 0.5766 (pt0) REVERT: B 24 MET cc_start: 0.6947 (mmm) cc_final: 0.6394 (mmm) REVERT: B 63 ILE cc_start: 0.6631 (OUTLIER) cc_final: 0.6314 (tt) REVERT: B 114 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.5997 (pt0) REVERT: B 183 ASP cc_start: 0.7858 (t0) cc_final: 0.7463 (t0) REVERT: B 320 GLU cc_start: 0.6489 (mm-30) cc_final: 0.6191 (mp0) REVERT: C 24 MET cc_start: 0.7722 (mmm) cc_final: 0.7485 (mmp) REVERT: C 83 MET cc_start: 0.8936 (tpt) cc_final: 0.7265 (tpt) REVERT: C 121 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6790 (mp) REVERT: D 313 ASN cc_start: 0.6946 (m110) cc_final: 0.6564 (m110) outliers start: 46 outliers final: 15 residues processed: 202 average time/residue: 1.3635 time to fit residues: 301.2971 Evaluate side-chains 171 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 46 LYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain B residue 10 ILE 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 305 MET Chi-restraints excluded: chain C residue 50 GLU 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 D residue 67 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 95 LEU 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 114 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 31 optimal weight: 0.0170 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 348 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN B 241 ASN B 278 HIS B 357 ASN D 11 ASN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.190086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.165696 restraints weight = 15965.742| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.23 r_work: 0.3785 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12481 Z= 0.157 Angle : 0.616 9.091 16884 Z= 0.296 Chirality : 0.042 0.231 1824 Planarity : 0.004 0.050 2144 Dihedral : 13.081 135.450 2125 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.83 % Allowed : 18.00 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1540 helix: 0.90 (0.18), residues: 820 sheet: -1.05 (0.42), residues: 116 loop : -0.79 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 166 HIS 0.005 0.001 HIS A 79 PHE 0.014 0.001 PHE C 290 TYR 0.010 0.001 TYR A 312 ARG 0.006 0.001 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 652) hydrogen bonds : angle 4.49003 ( 1875) covalent geometry : bond 0.00359 (12480) covalent geometry : angle 0.61645 (16884) Misc. bond : bond 0.00005 ( 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 210 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6590 (tpt90) REVERT: A 22 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.5885 (mp10) REVERT: A 49 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7402 (tpt170) REVERT: A 150 LYS cc_start: 0.7840 (ptpp) cc_final: 0.7325 (tttm) REVERT: A 196 PHE cc_start: 0.7365 (m-80) cc_final: 0.6956 (m-80) REVERT: A 242 LYS cc_start: 0.7611 (mptt) cc_final: 0.7255 (mmpt) REVERT: A 358 ASP cc_start: 0.7916 (m-30) cc_final: 0.7318 (t0) REVERT: A 379 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: B 16 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6817 (mp0) REVERT: B 22 GLN cc_start: 0.6277 (mm-40) cc_final: 0.5676 (pt0) REVERT: B 24 MET cc_start: 0.6997 (mmm) cc_final: 0.6603 (mmm) REVERT: B 63 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6272 (tt) REVERT: B 114 GLU cc_start: 0.6728 (pp20) cc_final: 0.6056 (pt0) REVERT: B 183 ASP cc_start: 0.7899 (t0) cc_final: 0.7591 (t0) REVERT: B 289 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.6822 (m-70) REVERT: B 320 GLU cc_start: 0.6421 (mm-30) cc_final: 0.6146 (mp0) REVERT: C 24 MET cc_start: 0.7751 (mmm) cc_final: 0.7525 (mmp) REVERT: C 83 MET cc_start: 0.8945 (tpt) cc_final: 0.7242 (tpt) REVERT: C 121 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6795 (mp) REVERT: D 313 ASN cc_start: 0.6870 (m110) cc_final: 0.6456 (m110) outliers start: 47 outliers final: 13 residues processed: 201 average time/residue: 1.5130 time to fit residues: 334.9809 Evaluate side-chains 164 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 49 ARG 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 10 ILE 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 289 HIS 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 D residue 67 VAL Chi-restraints excluded: chain D residue 93 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 72 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 169 ASN B 267 GLN C 107 GLN C 278 HIS ** C 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.185933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.160686 restraints weight = 16165.724| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.27 r_work: 0.3731 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12481 Z= 0.206 Angle : 0.691 10.951 16884 Z= 0.331 Chirality : 0.044 0.269 1824 Planarity : 0.005 0.049 2144 Dihedral : 12.852 134.752 2125 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.34 % Allowed : 19.79 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1540 helix: 0.72 (0.18), residues: 820 sheet: -0.95 (0.44), residues: 116 loop : -0.94 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 166 HIS 0.006 0.001 HIS A 79 PHE 0.019 0.002 PHE C 290 TYR 0.013 0.002 TYR A 312 ARG 0.006 0.001 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.04987 ( 652) hydrogen bonds : angle 4.62927 ( 1875) covalent geometry : bond 0.00488 (12480) covalent geometry : angle 0.69127 (16884) Misc. bond : bond 0.00064 ( 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 196 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6697 (tpt90) REVERT: A 22 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.5850 (mp10) REVERT: A 37 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.6847 (tp40) REVERT: A 150 LYS cc_start: 0.7954 (ptpp) cc_final: 0.7451 (tttm) REVERT: A 157 HIS cc_start: 0.6898 (OUTLIER) cc_final: 0.6483 (m-70) REVERT: A 196 PHE cc_start: 0.7428 (m-80) cc_final: 0.7108 (m-80) REVERT: A 242 LYS cc_start: 0.7663 (mptt) cc_final: 0.7292 (mmpt) REVERT: A 358 ASP cc_start: 0.7980 (m-30) cc_final: 0.7390 (t0) REVERT: A 379 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: B 22 GLN cc_start: 0.6283 (mm-40) cc_final: 0.5690 (pt0) REVERT: B 24 MET cc_start: 0.7001 (mmm) cc_final: 0.6685 (mmm) REVERT: B 63 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6348 (tt) REVERT: B 114 GLU cc_start: 0.6796 (pp20) cc_final: 0.6105 (pt0) REVERT: B 320 GLU cc_start: 0.6366 (mm-30) cc_final: 0.6014 (mp0) REVERT: C 22 GLN cc_start: 0.7114 (mm-40) cc_final: 0.6398 (tt0) REVERT: C 24 MET cc_start: 0.7725 (mmm) cc_final: 0.7470 (mmp) REVERT: C 83 MET cc_start: 0.8979 (tpt) cc_final: 0.7289 (tpt) outliers start: 41 outliers final: 15 residues processed: 187 average time/residue: 1.1919 time to fit residues: 243.9189 Evaluate side-chains 161 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 157 HIS 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 10 ILE 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 247 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 D residue 67 VAL Chi-restraints excluded: chain D residue 93 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 258 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 161 ASN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 106 ASN C 107 GLN C 390 ASN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.190339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165953 restraints weight = 16275.950| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.27 r_work: 0.3786 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12481 Z= 0.118 Angle : 0.585 10.472 16884 Z= 0.281 Chirality : 0.040 0.197 1824 Planarity : 0.004 0.057 2144 Dihedral : 12.225 132.208 2125 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.61 % Allowed : 21.66 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1540 helix: 1.19 (0.19), residues: 820 sheet: -0.98 (0.43), residues: 116 loop : -0.82 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 166 HIS 0.004 0.001 HIS A 79 PHE 0.008 0.001 PHE B 389 TYR 0.007 0.001 TYR A 312 ARG 0.007 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 652) hydrogen bonds : angle 4.37494 ( 1875) covalent geometry : bond 0.00269 (12480) covalent geometry : angle 0.58514 (16884) Misc. bond : bond 0.00011 ( 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: 32 poor density : 155 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6594 (tpt90) REVERT: A 22 GLN cc_start: 0.6186 (OUTLIER) cc_final: 0.5858 (mp10) REVERT: A 37 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.6760 (tp40) REVERT: A 150 LYS cc_start: 0.7897 (ptpp) cc_final: 0.7498 (tttm) REVERT: A 196 PHE cc_start: 0.7423 (m-80) cc_final: 0.7107 (m-80) REVERT: A 358 ASP cc_start: 0.7962 (m-30) cc_final: 0.7362 (t0) REVERT: B 22 GLN cc_start: 0.6220 (mm-40) cc_final: 0.5593 (pt0) REVERT: B 24 MET cc_start: 0.6981 (mmm) cc_final: 0.6708 (mmm) REVERT: B 63 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6249 (tt) REVERT: B 114 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6093 (pt0) REVERT: B 320 GLU cc_start: 0.6337 (mm-30) cc_final: 0.6051 (mp0) REVERT: C 22 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6463 (tt0) REVERT: D 135 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.5739 (ptt) REVERT: D 313 ASN cc_start: 0.6876 (m110) cc_final: 0.6308 (m110) REVERT: D 387 ARG cc_start: 0.6659 (mtt-85) cc_final: 0.6351 (mtt90) outliers start: 32 outliers final: 9 residues processed: 181 average time/residue: 1.2815 time to fit residues: 252.3047 Evaluate side-chains 154 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 153 LYS 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 C residue 137 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 160 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 85 optimal weight: 0.0970 chunk 135 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 117 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 11 ASN D 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.191969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.167765 restraints weight = 16214.346| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.25 r_work: 0.3802 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12481 Z= 0.107 Angle : 0.568 11.497 16884 Z= 0.272 Chirality : 0.039 0.190 1824 Planarity : 0.004 0.053 2144 Dihedral : 11.769 128.284 2125 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.61 % Allowed : 22.23 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1540 helix: 1.32 (0.19), residues: 828 sheet: -0.96 (0.43), residues: 116 loop : -0.65 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 166 HIS 0.003 0.000 HIS D 100 PHE 0.009 0.001 PHE B 389 TYR 0.012 0.001 TYR D 310 ARG 0.006 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 652) hydrogen bonds : angle 4.24281 ( 1875) covalent geometry : bond 0.00240 (12480) covalent geometry : angle 0.56786 (16884) Misc. bond : bond 0.00018 ( 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 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6485 (tpt90) REVERT: A 22 GLN cc_start: 0.6157 (OUTLIER) cc_final: 0.5835 (mp10) REVERT: A 150 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7633 (tttm) REVERT: A 191 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8053 (mmt90) REVERT: A 196 PHE cc_start: 0.7444 (m-80) cc_final: 0.7111 (m-80) REVERT: A 216 MET cc_start: 0.8832 (mmp) cc_final: 0.8433 (mmt) REVERT: A 358 ASP cc_start: 0.7948 (m-30) cc_final: 0.7378 (t0) REVERT: B 22 GLN cc_start: 0.6127 (mm-40) cc_final: 0.5451 (pt0) REVERT: B 24 MET cc_start: 0.7054 (mmm) cc_final: 0.6747 (mmm) REVERT: B 63 ILE cc_start: 0.6550 (OUTLIER) cc_final: 0.6232 (tt) REVERT: B 114 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6101 (pt0) REVERT: B 320 GLU cc_start: 0.6349 (mm-30) cc_final: 0.6075 (mp0) REVERT: C 22 GLN cc_start: 0.7149 (mm-40) cc_final: 0.6473 (tt0) REVERT: D 107 GLN cc_start: 0.5035 (OUTLIER) cc_final: 0.4741 (tp40) REVERT: D 272 HIS cc_start: 0.6874 (m170) cc_final: 0.6492 (m170) REVERT: D 313 ASN cc_start: 0.6743 (m110) cc_final: 0.6252 (m110) REVERT: D 387 ARG cc_start: 0.6597 (mtt-85) cc_final: 0.6265 (mtt90) outliers start: 32 outliers final: 10 residues processed: 190 average time/residue: 1.1434 time to fit residues: 238.4298 Evaluate side-chains 170 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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 247 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 93 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 79 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 11 ASN ** 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 = 0.4148 r_free = 0.4148 target = 0.191635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167039 restraints weight = 16281.855| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.27 r_work: 0.3799 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4560 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= 0.115 Angle : 0.595 11.482 16884 Z= 0.283 Chirality : 0.040 0.202 1824 Planarity : 0.004 0.059 2144 Dihedral : 11.548 124.163 2125 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.95 % Allowed : 23.78 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1540 helix: 1.30 (0.18), residues: 832 sheet: -0.92 (0.43), residues: 116 loop : -0.62 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 166 HIS 0.003 0.000 HIS A 79 PHE 0.020 0.001 PHE D 196 TYR 0.008 0.001 TYR B 97 ARG 0.010 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 652) hydrogen bonds : angle 4.24839 ( 1875) covalent geometry : bond 0.00263 (12480) covalent geometry : angle 0.59457 (16884) Misc. bond : bond 0.00021 ( 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 185 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6574 (tpt90) REVERT: A 22 GLN cc_start: 0.6167 (OUTLIER) cc_final: 0.5841 (mp10) REVERT: A 150 LYS cc_start: 0.7918 (ptpp) cc_final: 0.7643 (tttm) REVERT: A 196 PHE cc_start: 0.7462 (m-80) cc_final: 0.7078 (m-80) REVERT: A 358 ASP cc_start: 0.7934 (m-30) cc_final: 0.7344 (t0) REVERT: B 22 GLN cc_start: 0.6186 (mm-40) cc_final: 0.5502 (pt0) REVERT: B 24 MET cc_start: 0.7086 (mmm) cc_final: 0.6802 (mmm) REVERT: B 63 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6241 (tt) REVERT: B 114 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6096 (pt0) REVERT: B 320 GLU cc_start: 0.6354 (mm-30) cc_final: 0.6046 (mp0) REVERT: C 318 CYS cc_start: 0.7494 (m) cc_final: 0.7200 (t) REVERT: D 272 HIS cc_start: 0.6898 (m170) cc_final: 0.6429 (m170) REVERT: D 313 ASN cc_start: 0.6662 (m110) cc_final: 0.6174 (m110) REVERT: D 387 ARG cc_start: 0.6553 (mtt-85) cc_final: 0.6266 (mtt90) outliers start: 24 outliers final: 11 residues processed: 179 average time/residue: 1.2254 time to fit residues: 239.2783 Evaluate side-chains 164 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 153 LYS 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 247 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 93 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 30 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.191273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166871 restraints weight = 16249.960| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.26 r_work: 0.3797 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12481 Z= 0.120 Angle : 0.599 12.050 16884 Z= 0.286 Chirality : 0.041 0.195 1824 Planarity : 0.004 0.053 2144 Dihedral : 11.405 120.114 2125 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.04 % Allowed : 24.10 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1540 helix: 1.31 (0.18), residues: 832 sheet: -0.89 (0.43), residues: 116 loop : -0.61 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 166 HIS 0.004 0.000 HIS A 79 PHE 0.018 0.001 PHE D 196 TYR 0.018 0.001 TYR D 310 ARG 0.011 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 652) hydrogen bonds : angle 4.21920 ( 1875) covalent geometry : bond 0.00277 (12480) covalent geometry : angle 0.59938 (16884) Misc. bond : bond 0.00027 ( 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 176 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6570 (tpt90) REVERT: A 22 GLN cc_start: 0.6176 (OUTLIER) cc_final: 0.5856 (mp10) REVERT: A 150 LYS cc_start: 0.7920 (ptpp) cc_final: 0.7657 (tttm) REVERT: A 196 PHE cc_start: 0.7439 (m-80) cc_final: 0.7118 (m-80) REVERT: A 216 MET cc_start: 0.8781 (mmp) cc_final: 0.8400 (mmt) REVERT: A 358 ASP cc_start: 0.7938 (m-30) cc_final: 0.7349 (t0) REVERT: B 22 GLN cc_start: 0.6199 (mm-40) cc_final: 0.5495 (pt0) REVERT: B 24 MET cc_start: 0.7107 (mmm) cc_final: 0.6843 (mmm) REVERT: B 63 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.6237 (tt) REVERT: B 114 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6153 (pt0) REVERT: B 320 GLU cc_start: 0.6352 (mm-30) cc_final: 0.6031 (mp0) REVERT: C 22 GLN cc_start: 0.7142 (mm-40) cc_final: 0.6425 (tt0) REVERT: D 135 MET cc_start: 0.6363 (ptt) cc_final: 0.6090 (ttp) REVERT: D 272 HIS cc_start: 0.6905 (m170) cc_final: 0.6440 (m170) REVERT: D 313 ASN cc_start: 0.6629 (m110) cc_final: 0.6166 (m110) REVERT: D 387 ARG cc_start: 0.6518 (mtt-85) cc_final: 0.6185 (mtt90) outliers start: 25 outliers final: 14 residues processed: 169 average time/residue: 1.2209 time to fit residues: 225.7208 Evaluate side-chains 166 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 153 LYS 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 247 LEU 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 D residue 54 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 93 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 115 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 126 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- 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 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN D 54 GLN D 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.188525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164304 restraints weight = 16217.471| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.23 r_work: 0.3778 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12481 Z= 0.148 Angle : 0.630 11.345 16884 Z= 0.301 Chirality : 0.042 0.214 1824 Planarity : 0.004 0.051 2144 Dihedral : 11.463 116.689 2125 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.87 % Allowed : 24.76 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1540 helix: 1.21 (0.18), residues: 832 sheet: -0.85 (0.44), residues: 116 loop : -0.65 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 166 HIS 0.005 0.001 HIS B 278 PHE 0.018 0.001 PHE D 196 TYR 0.022 0.001 TYR D 310 ARG 0.010 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 652) hydrogen bonds : angle 4.25566 ( 1875) covalent geometry : bond 0.00349 (12480) covalent geometry : angle 0.63019 (16884) Misc. bond : bond 0.00020 ( 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 177 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6611 (tpt90) REVERT: A 22 GLN cc_start: 0.6219 (OUTLIER) cc_final: 0.5899 (mp10) REVERT: A 150 LYS cc_start: 0.7924 (ptpp) cc_final: 0.7650 (tttm) REVERT: A 196 PHE cc_start: 0.7469 (m-80) cc_final: 0.7171 (m-80) REVERT: A 358 ASP cc_start: 0.7938 (m-30) cc_final: 0.7388 (t0) REVERT: B 22 GLN cc_start: 0.6165 (mm-40) cc_final: 0.5459 (pt0) REVERT: B 24 MET cc_start: 0.7148 (mmm) cc_final: 0.6873 (mmm) REVERT: B 114 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6157 (pt0) REVERT: B 320 GLU cc_start: 0.6315 (mm-30) cc_final: 0.6055 (mp0) REVERT: C 22 GLN cc_start: 0.7151 (mm-40) cc_final: 0.6461 (tt0) REVERT: D 135 MET cc_start: 0.6659 (ptt) cc_final: 0.6445 (ttp) REVERT: D 272 HIS cc_start: 0.6896 (m170) cc_final: 0.6411 (m170) REVERT: D 313 ASN cc_start: 0.6746 (m110) cc_final: 0.6241 (m110) REVERT: D 387 ARG cc_start: 0.6557 (mtt-85) cc_final: 0.6218 (mtt90) outliers start: 23 outliers final: 16 residues processed: 170 average time/residue: 1.2347 time to fit residues: 229.6193 Evaluate side-chains 170 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 153 LYS Chi-restraints excluded: chain A residue 273 THR 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 247 LEU Chi-restraints excluded: chain C residue 172 ASP 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 D residue 54 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 93 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 1 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 0.0010 chunk 86 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.191087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.166936 restraints weight = 16188.996| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.25 r_work: 0.3796 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12481 Z= 0.117 Angle : 0.600 11.914 16884 Z= 0.287 Chirality : 0.041 0.193 1824 Planarity : 0.004 0.055 2144 Dihedral : 11.315 114.204 2125 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.87 % Allowed : 24.76 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1540 helix: 1.30 (0.18), residues: 836 sheet: -0.85 (0.44), residues: 116 loop : -0.70 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 166 HIS 0.003 0.001 HIS A 79 PHE 0.008 0.001 PHE B 196 TYR 0.027 0.001 TYR D 310 ARG 0.006 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 652) hydrogen bonds : angle 4.19861 ( 1875) covalent geometry : bond 0.00268 (12480) covalent geometry : angle 0.59958 (16884) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7887.74 seconds wall clock time: 138 minutes 11.99 seconds (8291.99 seconds total)