Starting phenix.real_space_refine on Sun May 3 02:06:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yab_72726/05_2026/9yab_72726.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yab_72726/05_2026/9yab_72726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yab_72726/05_2026/9yab_72726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yab_72726/05_2026/9yab_72726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yab_72726/05_2026/9yab_72726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yab_72726/05_2026/9yab_72726.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 65 5.16 5 C 6066 2.51 5 N 1657 2.21 5 O 1893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9687 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3369 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain: "K" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 12, 'TRANS': 338} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.34, per 1000 atoms: 0.24 Number of scatterers: 9687 At special positions: 0 Unit cell: (75.166, 108.206, 113.162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 5 15.00 Mg 1 11.99 O 1893 8.00 N 1657 7.00 C 6066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 400.1 milliseconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 47.7% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.643A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 43 removed outlier: 3.775A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.383A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.558A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.574A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.142A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 295 through 301 Proline residue: A 298 - end of helix removed outlier: 3.585A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 301' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.507A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.826A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.717A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 4.053A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.160A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.698A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.832A pdb=" N GLY B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.829A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.551A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.632A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.127A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.232A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 removed outlier: 3.536A pdb=" N ARG K 22 " --> pdb=" O ARG K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 88 removed outlier: 4.713A pdb=" N GLU K 79 " --> pdb=" O ARG K 75 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET K 81 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 134 removed outlier: 3.775A pdb=" N GLN K 121 " --> pdb=" O GLY K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 203 Processing helix chain 'K' and resid 262 through 290 removed outlier: 3.609A pdb=" N GLY K 268 " --> pdb=" O ARG K 264 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER K 274 " --> pdb=" O ASN K 270 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 Processing helix chain 'K' and resid 337 through 351 removed outlier: 3.872A pdb=" N ALA K 351 " --> pdb=" O TYR K 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.025A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.011A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'K' and resid 54 through 57 removed outlier: 8.849A pdb=" N TYR K 54 " --> pdb=" O VAL K 6 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL K 8 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N TYR K 56 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL K 10 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR K 96 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N THR K 238 " --> pdb=" O ARG K 229 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG K 229 " --> pdb=" O THR K 238 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS K 240 " --> pdb=" O GLN K 227 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN K 227 " --> pdb=" O LYS K 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 54 through 57 removed outlier: 8.849A pdb=" N TYR K 54 " --> pdb=" O VAL K 6 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL K 8 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N TYR K 56 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL K 10 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR K 96 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N THR K 238 " --> pdb=" O ARG K 229 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG K 229 " --> pdb=" O THR K 238 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS K 240 " --> pdb=" O GLN K 227 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN K 227 " --> pdb=" O LYS K 240 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL K 142 " --> pdb=" O VAL K 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA9, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AB1, first strand: chain 'K' and resid 205 through 206 485 hydrogen bonds defined for protein. 1398 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: 1.75 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1758 1.32 - 1.45: 2564 1.45 - 1.57: 5455 1.57 - 1.69: 12 1.69 - 1.82: 105 Bond restraints: 9894 Sorted by residual: bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 4.04e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.53e+00 bond pdb=" CB GLN A 358 " pdb=" CG GLN A 358 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CA LYS K 44 " pdb=" CB LYS K 44 " ideal model delta sigma weight residual 1.530 1.555 -0.024 1.69e-02 3.50e+03 2.08e+00 bond pdb=" CB ASP A 322 " pdb=" CG ASP A 322 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.97e+00 ... (remaining 9889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 13004 1.72 - 3.43: 308 3.43 - 5.15: 91 5.15 - 6.86: 18 6.86 - 8.58: 4 Bond angle restraints: 13425 Sorted by residual: angle pdb=" CB LYS B 336 " pdb=" CG LYS B 336 " pdb=" CD LYS B 336 " ideal model delta sigma weight residual 111.30 119.88 -8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CA LYS B 336 " pdb=" CB LYS B 336 " pdb=" CG LYS B 336 " ideal model delta sigma weight residual 114.10 121.00 -6.90 2.00e+00 2.50e-01 1.19e+01 angle pdb=" CA MET K 210 " pdb=" CB MET K 210 " pdb=" CG MET K 210 " ideal model delta sigma weight residual 114.10 119.78 -5.68 2.00e+00 2.50e-01 8.05e+00 angle pdb=" CA LYS K 44 " pdb=" CB LYS K 44 " pdb=" CG LYS K 44 " ideal model delta sigma weight residual 114.10 119.72 -5.62 2.00e+00 2.50e-01 7.89e+00 angle pdb=" CA GLU B 410 " pdb=" CB GLU B 410 " pdb=" CG GLU B 410 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.82e+00 ... (remaining 13420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.04: 5735 29.04 - 58.08: 246 58.08 - 87.12: 30 87.12 - 116.16: 0 116.16 - 145.20: 1 Dihedral angle restraints: 6012 sinusoidal: 2480 harmonic: 3532 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -40.61 145.20 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" CA GLU K 233 " pdb=" C GLU K 233 " pdb=" N THR K 234 " pdb=" CA THR K 234 " ideal model delta harmonic sigma weight residual -180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -8.72 77.99 1 2.00e+01 2.50e-03 1.90e+01 ... (remaining 6009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1122 0.046 - 0.091: 253 0.091 - 0.137: 92 0.137 - 0.182: 6 0.182 - 0.228: 1 Chirality restraints: 1474 Sorted by residual: chirality pdb=" C10 TA1 B 502 " pdb=" C02 TA1 B 502 " pdb=" C11 TA1 B 502 " pdb=" C18 TA1 B 502 " both_signs ideal model delta sigma weight residual False 2.54 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C21 TA1 B 502 " pdb=" C20 TA1 B 502 " pdb=" C24 TA1 B 502 " pdb=" O09 TA1 B 502 " both_signs ideal model delta sigma weight residual False -2.30 -2.13 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA ILE K 304 " pdb=" N ILE K 304 " pdb=" C ILE K 304 " pdb=" CB ILE K 304 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 1471 not shown) Planarity restraints: 1744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " -0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO A 89 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 415 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" CD GLU A 415 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU A 415 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 415 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 380 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ARG B 380 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG B 380 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE B 381 " 0.014 2.00e-02 2.50e+03 ... (remaining 1741 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 44 2.66 - 3.22: 9350 3.22 - 3.78: 14549 3.78 - 4.34: 20746 4.34 - 4.90: 34585 Nonbonded interactions: 79274 Sorted by model distance: nonbonded pdb=" OD2 ASP A 98 " pdb="MG MG A 502 " model vdw 2.095 2.170 nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.224 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.330 2.170 nonbonded pdb=" PB GTP A 501 " pdb="MG MG A 502 " model vdw 2.373 2.530 nonbonded pdb=" OE1 GLU A 71 " pdb="MG MG A 502 " model vdw 2.382 2.170 ... (remaining 79269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.220 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.004 0.044 9894 Z= 0.177 Angle : 0.722 8.577 13425 Z= 0.368 Chirality : 0.044 0.228 1474 Planarity : 0.005 0.062 1744 Dihedral : 15.685 145.201 3744 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.95 % Allowed : 11.34 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.24), residues: 1211 helix: 0.64 (0.23), residues: 476 sheet: -0.88 (0.34), residues: 232 loop : -1.14 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 254 TYR 0.011 0.001 TYR K 74 PHE 0.015 0.001 PHE K 303 TRP 0.014 0.002 TRP K 350 HIS 0.002 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9894) covalent geometry : angle 0.72166 (13425) hydrogen bonds : bond 0.16432 ( 455) hydrogen bonds : angle 6.78511 ( 1398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6291 (mttt) cc_final: 0.5646 (mttt) REVERT: A 338 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8709 (mmmt) REVERT: B 26 ASP cc_start: 0.7922 (t0) cc_final: 0.7570 (t0) REVERT: B 48 ASN cc_start: 0.8627 (p0) cc_final: 0.8380 (p0) REVERT: B 145 SER cc_start: 0.8503 (m) cc_final: 0.8275 (p) REVERT: B 299 MET cc_start: 0.8510 (mmt) cc_final: 0.8128 (mmt) REVERT: B 323 MET cc_start: 0.8270 (mmm) cc_final: 0.8023 (mmm) REVERT: B 355 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7609 (t0) REVERT: B 364 SER cc_start: 0.8916 (p) cc_final: 0.8657 (m) REVERT: K 25 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7382 (tppt) REVERT: K 59 HIS cc_start: 0.7090 (t-170) cc_final: 0.6812 (t-170) REVERT: K 67 TYR cc_start: 0.8509 (t80) cc_final: 0.8255 (t80) REVERT: K 72 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7940 (tm-30) REVERT: K 86 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: K 89 TYR cc_start: 0.8382 (m-80) cc_final: 0.8163 (m-80) REVERT: K 123 CYS cc_start: 0.8898 (m) cc_final: 0.8614 (m) REVERT: K 167 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7986 (ptm160) outliers start: 10 outliers final: 6 residues processed: 179 average time/residue: 0.1037 time to fit residues: 25.8718 Evaluate side-chains 166 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 248 ASP Chi-restraints excluded: chain K residue 343 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101827 restraints weight = 14931.528| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.92 r_work: 0.3173 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9894 Z= 0.178 Angle : 0.566 6.664 13425 Z= 0.289 Chirality : 0.044 0.260 1474 Planarity : 0.004 0.047 1744 Dihedral : 8.626 146.115 1479 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.10 % Allowed : 10.87 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1211 helix: 1.44 (0.24), residues: 481 sheet: -0.50 (0.34), residues: 228 loop : -1.07 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 121 TYR 0.015 0.001 TYR K 74 PHE 0.015 0.001 PHE A 49 TRP 0.018 0.002 TRP A 21 HIS 0.002 0.001 HIS K 59 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9894) covalent geometry : angle 0.56633 (13425) hydrogen bonds : bond 0.04609 ( 455) hydrogen bonds : angle 4.64581 ( 1398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6385 (mttt) cc_final: 0.5515 (mttt) REVERT: A 429 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7905 (mt-10) REVERT: B 26 ASP cc_start: 0.8716 (t0) cc_final: 0.8309 (t0) REVERT: B 48 ASN cc_start: 0.8878 (p0) cc_final: 0.8606 (p0) REVERT: B 145 SER cc_start: 0.8803 (m) cc_final: 0.8371 (p) REVERT: B 170 MET cc_start: 0.8899 (mtt) cc_final: 0.8652 (mtt) REVERT: B 194 GLU cc_start: 0.8346 (mp0) cc_final: 0.7956 (mp0) REVERT: B 274 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7901 (m) REVERT: B 323 MET cc_start: 0.8501 (mmm) cc_final: 0.8181 (mmm) REVERT: B 364 SER cc_start: 0.9233 (OUTLIER) cc_final: 0.8830 (m) REVERT: B 390 ARG cc_start: 0.8763 (mtm110) cc_final: 0.8536 (ttp-110) REVERT: K 25 LYS cc_start: 0.7468 (mmtm) cc_final: 0.7142 (tppt) REVERT: K 67 TYR cc_start: 0.8778 (t80) cc_final: 0.8225 (t80) REVERT: K 72 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8161 (tm-30) REVERT: K 123 CYS cc_start: 0.9141 (m) cc_final: 0.8825 (m) REVERT: K 303 PHE cc_start: 0.8480 (t80) cc_final: 0.8190 (t80) outliers start: 22 outliers final: 10 residues processed: 185 average time/residue: 0.1094 time to fit residues: 27.8835 Evaluate side-chains 165 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 375 GLN B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101518 restraints weight = 15012.943| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.12 r_work: 0.3144 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9894 Z= 0.175 Angle : 0.550 6.139 13425 Z= 0.278 Chirality : 0.044 0.231 1474 Planarity : 0.004 0.042 1744 Dihedral : 8.358 147.539 1467 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.38 % Allowed : 11.73 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1211 helix: 1.59 (0.24), residues: 485 sheet: -0.29 (0.35), residues: 228 loop : -1.15 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.014 0.001 TYR A 357 PHE 0.015 0.001 PHE A 49 TRP 0.019 0.001 TRP A 21 HIS 0.002 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9894) covalent geometry : angle 0.55017 (13425) hydrogen bonds : bond 0.04293 ( 455) hydrogen bonds : angle 4.43186 ( 1398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6103 (mttt) cc_final: 0.5470 (mttt) REVERT: A 338 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8931 (mmmt) REVERT: B 26 ASP cc_start: 0.8850 (t0) cc_final: 0.8441 (t0) REVERT: B 48 ASN cc_start: 0.8804 (p0) cc_final: 0.8523 (p0) REVERT: B 145 SER cc_start: 0.8798 (m) cc_final: 0.8222 (p) REVERT: B 170 MET cc_start: 0.9026 (mtt) cc_final: 0.8770 (mtt) REVERT: B 323 MET cc_start: 0.8466 (mmm) cc_final: 0.8102 (mmm) REVERT: B 364 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8749 (m) REVERT: B 375 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: B 390 ARG cc_start: 0.8838 (mtm110) cc_final: 0.8617 (ttp-110) REVERT: K 25 LYS cc_start: 0.7404 (mmtm) cc_final: 0.7115 (tppt) REVERT: K 67 TYR cc_start: 0.8745 (t80) cc_final: 0.8096 (t80) REVERT: K 72 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8127 (tm-30) REVERT: K 123 CYS cc_start: 0.9129 (m) cc_final: 0.8816 (m) REVERT: K 303 PHE cc_start: 0.8378 (t80) cc_final: 0.8054 (t80) REVERT: K 349 ASP cc_start: 0.8640 (t0) cc_final: 0.8398 (t0) outliers start: 25 outliers final: 13 residues processed: 174 average time/residue: 0.1105 time to fit residues: 26.2366 Evaluate side-chains 166 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 227 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 0.0570 chunk 9 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.103739 restraints weight = 15010.450| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.13 r_work: 0.3163 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9894 Z= 0.122 Angle : 0.523 6.210 13425 Z= 0.263 Chirality : 0.043 0.224 1474 Planarity : 0.004 0.044 1744 Dihedral : 8.123 146.982 1463 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.10 % Allowed : 13.16 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.25), residues: 1211 helix: 1.77 (0.24), residues: 486 sheet: -0.14 (0.35), residues: 228 loop : -1.13 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 309 TYR 0.017 0.001 TYR A 357 PHE 0.011 0.001 PHE A 49 TRP 0.019 0.001 TRP A 21 HIS 0.002 0.000 HIS K 59 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9894) covalent geometry : angle 0.52314 (13425) hydrogen bonds : bond 0.03774 ( 455) hydrogen bonds : angle 4.24167 ( 1398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6056 (mttt) cc_final: 0.5477 (mttt) REVERT: A 338 LYS cc_start: 0.9091 (mmmm) cc_final: 0.8833 (mmmt) REVERT: B 26 ASP cc_start: 0.8876 (t0) cc_final: 0.8473 (t0) REVERT: B 48 ASN cc_start: 0.8785 (p0) cc_final: 0.8499 (p0) REVERT: B 145 SER cc_start: 0.8807 (m) cc_final: 0.8168 (p) REVERT: B 323 MET cc_start: 0.8440 (mmm) cc_final: 0.8087 (mmm) REVERT: B 364 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8799 (m) REVERT: B 390 ARG cc_start: 0.8786 (mtm110) cc_final: 0.8575 (ttp-110) REVERT: B 426 GLN cc_start: 0.8340 (tp40) cc_final: 0.7921 (tp40) REVERT: K 25 LYS cc_start: 0.7371 (mmtm) cc_final: 0.7099 (tppt) REVERT: K 67 TYR cc_start: 0.8614 (t80) cc_final: 0.7931 (t80) REVERT: K 72 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8143 (tm-30) REVERT: K 123 CYS cc_start: 0.9111 (m) cc_final: 0.8795 (m) REVERT: K 285 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8508 (mm) REVERT: K 303 PHE cc_start: 0.8366 (t80) cc_final: 0.8056 (t80) REVERT: K 349 ASP cc_start: 0.8640 (t0) cc_final: 0.8435 (t0) outliers start: 22 outliers final: 16 residues processed: 174 average time/residue: 0.1074 time to fit residues: 25.7573 Evaluate side-chains 170 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 248 ASP Chi-restraints excluded: chain K residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 77 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 66 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 384 GLN B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102760 restraints weight = 15130.075| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.13 r_work: 0.3153 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9894 Z= 0.138 Angle : 0.529 6.210 13425 Z= 0.265 Chirality : 0.043 0.212 1474 Planarity : 0.004 0.044 1744 Dihedral : 8.064 147.372 1463 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.67 % Allowed : 12.96 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.25), residues: 1211 helix: 1.80 (0.24), residues: 486 sheet: -0.08 (0.35), residues: 231 loop : -1.15 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 309 TYR 0.017 0.001 TYR A 357 PHE 0.012 0.001 PHE A 49 TRP 0.017 0.001 TRP A 21 HIS 0.002 0.000 HIS K 59 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9894) covalent geometry : angle 0.52947 (13425) hydrogen bonds : bond 0.03762 ( 455) hydrogen bonds : angle 4.19450 ( 1398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.5508 (tttt) cc_final: 0.5138 (tttm) REVERT: A 326 LYS cc_start: 0.6001 (mttt) cc_final: 0.5444 (mttt) REVERT: A 338 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8890 (mmmt) REVERT: B 26 ASP cc_start: 0.8886 (t0) cc_final: 0.8480 (t0) REVERT: B 48 ASN cc_start: 0.8774 (p0) cc_final: 0.8525 (p0) REVERT: B 145 SER cc_start: 0.8817 (m) cc_final: 0.8143 (p) REVERT: B 323 MET cc_start: 0.8455 (mmm) cc_final: 0.8118 (mmm) REVERT: B 364 SER cc_start: 0.9263 (OUTLIER) cc_final: 0.8790 (m) REVERT: B 390 ARG cc_start: 0.8857 (mtm110) cc_final: 0.8646 (ttp-110) REVERT: B 426 GLN cc_start: 0.8314 (tp40) cc_final: 0.7901 (tp40) REVERT: K 25 LYS cc_start: 0.7364 (mmtm) cc_final: 0.7139 (tppt) REVERT: K 67 TYR cc_start: 0.8570 (t80) cc_final: 0.7915 (t80) REVERT: K 72 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8189 (tm-30) REVERT: K 76 ASP cc_start: 0.8325 (t0) cc_final: 0.8012 (t0) REVERT: K 123 CYS cc_start: 0.9109 (m) cc_final: 0.8796 (m) REVERT: K 285 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8495 (mm) REVERT: K 303 PHE cc_start: 0.8379 (t80) cc_final: 0.8135 (t80) outliers start: 28 outliers final: 18 residues processed: 187 average time/residue: 0.1090 time to fit residues: 28.0318 Evaluate side-chains 175 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 248 ASP Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 77 optimal weight: 0.0970 chunk 80 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN K 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104312 restraints weight = 15091.886| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.02 r_work: 0.3177 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9894 Z= 0.125 Angle : 0.533 6.773 13425 Z= 0.266 Chirality : 0.042 0.214 1474 Planarity : 0.004 0.045 1744 Dihedral : 7.988 147.779 1463 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.91 % Allowed : 14.39 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1211 helix: 1.82 (0.24), residues: 488 sheet: 0.00 (0.35), residues: 231 loop : -1.13 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 309 TYR 0.012 0.001 TYR K 74 PHE 0.011 0.001 PHE A 49 TRP 0.017 0.001 TRP A 21 HIS 0.001 0.000 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9894) covalent geometry : angle 0.53264 (13425) hydrogen bonds : bond 0.03612 ( 455) hydrogen bonds : angle 4.14827 ( 1398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7995 (tm-30) REVERT: A 60 LYS cc_start: 0.5456 (tttt) cc_final: 0.5089 (tttm) REVERT: A 326 LYS cc_start: 0.6131 (mttt) cc_final: 0.5552 (mttt) REVERT: A 338 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8849 (mmmt) REVERT: B 26 ASP cc_start: 0.8864 (t0) cc_final: 0.8465 (t0) REVERT: B 48 ASN cc_start: 0.8810 (p0) cc_final: 0.8527 (p0) REVERT: B 145 SER cc_start: 0.8890 (m) cc_final: 0.8221 (p) REVERT: B 323 MET cc_start: 0.8431 (mmm) cc_final: 0.8125 (mmm) REVERT: B 363 MET cc_start: 0.7981 (ptp) cc_final: 0.7648 (ptp) REVERT: B 364 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.8801 (m) REVERT: B 380 ARG cc_start: 0.8403 (mtp180) cc_final: 0.8183 (ptm160) REVERT: B 426 GLN cc_start: 0.8289 (tp40) cc_final: 0.7956 (tp40) REVERT: K 25 LYS cc_start: 0.7489 (mmtm) cc_final: 0.7230 (tppt) REVERT: K 67 TYR cc_start: 0.8556 (t80) cc_final: 0.7904 (t80) REVERT: K 72 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8212 (tm-30) REVERT: K 76 ASP cc_start: 0.8308 (t0) cc_final: 0.8077 (t0) REVERT: K 123 CYS cc_start: 0.9147 (m) cc_final: 0.8840 (m) REVERT: K 285 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8566 (mm) outliers start: 20 outliers final: 16 residues processed: 174 average time/residue: 0.1122 time to fit residues: 26.6888 Evaluate side-chains 171 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 89 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103240 restraints weight = 15169.173| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.14 r_work: 0.3152 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9894 Z= 0.140 Angle : 0.546 6.644 13425 Z= 0.272 Chirality : 0.043 0.214 1474 Planarity : 0.004 0.044 1744 Dihedral : 7.957 148.080 1463 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.38 % Allowed : 14.59 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1211 helix: 1.75 (0.24), residues: 496 sheet: 0.08 (0.35), residues: 231 loop : -1.16 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 390 TYR 0.012 0.001 TYR K 74 PHE 0.012 0.001 PHE A 49 TRP 0.017 0.001 TRP A 21 HIS 0.002 0.001 HIS K 59 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9894) covalent geometry : angle 0.54642 (13425) hydrogen bonds : bond 0.03673 ( 455) hydrogen bonds : angle 4.11163 ( 1398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6018 (mttt) cc_final: 0.4831 (mttp) REVERT: A 338 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8773 (mmmt) REVERT: B 26 ASP cc_start: 0.8902 (t0) cc_final: 0.8495 (t0) REVERT: B 48 ASN cc_start: 0.8781 (p0) cc_final: 0.8489 (p0) REVERT: B 145 SER cc_start: 0.8892 (m) cc_final: 0.8203 (p) REVERT: B 323 MET cc_start: 0.8404 (mmm) cc_final: 0.8095 (mmm) REVERT: B 364 SER cc_start: 0.9262 (OUTLIER) cc_final: 0.8790 (m) REVERT: B 426 GLN cc_start: 0.8205 (tp40) cc_final: 0.7786 (tp40) REVERT: K 25 LYS cc_start: 0.7445 (mmtm) cc_final: 0.7189 (tppt) REVERT: K 67 TYR cc_start: 0.8591 (t80) cc_final: 0.7909 (t80) REVERT: K 72 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8195 (tm-30) REVERT: K 76 ASP cc_start: 0.8299 (t0) cc_final: 0.7962 (t0) REVERT: K 123 CYS cc_start: 0.9105 (m) cc_final: 0.8795 (m) REVERT: K 285 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8517 (mm) outliers start: 25 outliers final: 17 residues processed: 174 average time/residue: 0.1081 time to fit residues: 25.8960 Evaluate side-chains 171 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 0.0770 chunk 118 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 0.0000 chunk 3 optimal weight: 0.0970 chunk 34 optimal weight: 0.0980 overall best weight: 0.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107646 restraints weight = 14983.670| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.14 r_work: 0.3221 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9894 Z= 0.095 Angle : 0.521 8.036 13425 Z= 0.258 Chirality : 0.041 0.211 1474 Planarity : 0.004 0.045 1744 Dihedral : 7.735 150.766 1463 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.10 % Allowed : 15.06 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.25), residues: 1211 helix: 2.04 (0.24), residues: 488 sheet: 0.32 (0.34), residues: 236 loop : -1.13 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 254 TYR 0.012 0.001 TYR K 74 PHE 0.009 0.001 PHE K 303 TRP 0.018 0.002 TRP A 21 HIS 0.003 0.000 HIS K 59 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 9894) covalent geometry : angle 0.52133 (13425) hydrogen bonds : bond 0.03122 ( 455) hydrogen bonds : angle 3.93754 ( 1398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASP cc_start: 0.8382 (t0) cc_final: 0.8017 (m-30) REVERT: A 326 LYS cc_start: 0.5933 (mttt) cc_final: 0.5405 (mttt) REVERT: A 338 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8741 (mmmt) REVERT: B 26 ASP cc_start: 0.8869 (t0) cc_final: 0.8453 (t0) REVERT: B 48 ASN cc_start: 0.8826 (p0) cc_final: 0.8538 (p0) REVERT: B 145 SER cc_start: 0.8787 (m) cc_final: 0.8030 (p) REVERT: B 170 MET cc_start: 0.8850 (ptp) cc_final: 0.8489 (mtt) REVERT: B 299 MET cc_start: 0.8181 (mmt) cc_final: 0.7828 (mmt) REVERT: B 307 HIS cc_start: 0.8815 (m90) cc_final: 0.8376 (m90) REVERT: B 323 MET cc_start: 0.8348 (mmm) cc_final: 0.8040 (mmm) REVERT: B 363 MET cc_start: 0.7887 (ptp) cc_final: 0.7549 (ptp) REVERT: B 364 SER cc_start: 0.9212 (p) cc_final: 0.8772 (m) REVERT: B 426 GLN cc_start: 0.8062 (tp40) cc_final: 0.7713 (tp40) REVERT: K 25 LYS cc_start: 0.7471 (mmtm) cc_final: 0.7211 (tppt) REVERT: K 67 TYR cc_start: 0.8511 (t80) cc_final: 0.7884 (t80) REVERT: K 72 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8205 (tm-30) REVERT: K 76 ASP cc_start: 0.8269 (t0) cc_final: 0.7833 (t0) REVERT: K 123 CYS cc_start: 0.8999 (m) cc_final: 0.8692 (m) REVERT: K 285 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8441 (mm) outliers start: 22 outliers final: 14 residues processed: 183 average time/residue: 0.1024 time to fit residues: 26.0481 Evaluate side-chains 174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104380 restraints weight = 15032.933| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.04 r_work: 0.3172 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9894 Z= 0.151 Angle : 0.563 8.168 13425 Z= 0.280 Chirality : 0.043 0.211 1474 Planarity : 0.004 0.044 1744 Dihedral : 7.813 150.455 1463 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.72 % Allowed : 15.35 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1211 helix: 1.84 (0.24), residues: 496 sheet: 0.21 (0.35), residues: 231 loop : -1.13 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 390 TYR 0.035 0.001 TYR K 54 PHE 0.015 0.001 PHE A 49 TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9894) covalent geometry : angle 0.56326 (13425) hydrogen bonds : bond 0.03626 ( 455) hydrogen bonds : angle 4.02918 ( 1398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 60 LYS cc_start: 0.4819 (tttt) cc_final: 0.4264 (tttm) REVERT: A 326 LYS cc_start: 0.6054 (mttt) cc_final: 0.4860 (mttp) REVERT: B 26 ASP cc_start: 0.8869 (t0) cc_final: 0.8453 (t0) REVERT: B 48 ASN cc_start: 0.8799 (p0) cc_final: 0.8506 (p0) REVERT: B 145 SER cc_start: 0.8912 (m) cc_final: 0.8210 (p) REVERT: B 323 MET cc_start: 0.8376 (mmm) cc_final: 0.8087 (mmm) REVERT: B 363 MET cc_start: 0.8017 (ptp) cc_final: 0.7673 (ptp) REVERT: B 364 SER cc_start: 0.9246 (p) cc_final: 0.8791 (m) REVERT: B 426 GLN cc_start: 0.8043 (tp40) cc_final: 0.7685 (tp40) REVERT: K 25 LYS cc_start: 0.7495 (mmtm) cc_final: 0.7258 (tppt) REVERT: K 67 TYR cc_start: 0.8646 (t80) cc_final: 0.7963 (t80) REVERT: K 72 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8132 (tm-30) REVERT: K 76 ASP cc_start: 0.7954 (t0) cc_final: 0.7592 (t0) REVERT: K 123 CYS cc_start: 0.9082 (m) cc_final: 0.8771 (m) REVERT: K 285 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8553 (mm) outliers start: 18 outliers final: 16 residues processed: 175 average time/residue: 0.1092 time to fit residues: 26.5752 Evaluate side-chains 172 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 248 ASP Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 0.0010 chunk 108 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104852 restraints weight = 14990.328| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.03 r_work: 0.3183 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9894 Z= 0.129 Angle : 0.569 10.207 13425 Z= 0.281 Chirality : 0.043 0.210 1474 Planarity : 0.004 0.045 1744 Dihedral : 7.816 151.223 1463 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.53 % Allowed : 15.63 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1211 helix: 1.81 (0.24), residues: 496 sheet: 0.23 (0.35), residues: 231 loop : -1.11 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 254 TYR 0.040 0.001 TYR K 54 PHE 0.010 0.001 PHE K 303 TRP 0.016 0.001 TRP A 21 HIS 0.002 0.000 HIS K 230 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9894) covalent geometry : angle 0.56878 (13425) hydrogen bonds : bond 0.03458 ( 455) hydrogen bonds : angle 4.03625 ( 1398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 60 LYS cc_start: 0.4789 (tttt) cc_final: 0.4222 (tttm) REVERT: A 326 LYS cc_start: 0.6034 (mttt) cc_final: 0.5341 (mttt) REVERT: B 26 ASP cc_start: 0.8893 (t0) cc_final: 0.8480 (t0) REVERT: B 48 ASN cc_start: 0.8789 (p0) cc_final: 0.8498 (p0) REVERT: B 145 SER cc_start: 0.8883 (m) cc_final: 0.8154 (p) REVERT: B 307 HIS cc_start: 0.8862 (m90) cc_final: 0.8405 (m90) REVERT: B 323 MET cc_start: 0.8367 (mmm) cc_final: 0.8071 (mmm) REVERT: B 363 MET cc_start: 0.8025 (ptp) cc_final: 0.7630 (ptp) REVERT: B 364 SER cc_start: 0.9222 (p) cc_final: 0.8773 (m) REVERT: B 426 GLN cc_start: 0.7995 (tp40) cc_final: 0.7646 (tp40) REVERT: K 25 LYS cc_start: 0.7479 (mmtm) cc_final: 0.7230 (tppt) REVERT: K 67 TYR cc_start: 0.8585 (t80) cc_final: 0.7901 (t80) REVERT: K 72 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8058 (tm-30) REVERT: K 76 ASP cc_start: 0.7675 (t0) cc_final: 0.7332 (t0) REVERT: K 123 CYS cc_start: 0.9070 (m) cc_final: 0.8753 (m) outliers start: 16 outliers final: 14 residues processed: 180 average time/residue: 0.1031 time to fit residues: 26.1065 Evaluate side-chains 177 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 119 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.0370 chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105165 restraints weight = 14913.199| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.14 r_work: 0.3184 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9894 Z= 0.117 Angle : 0.569 9.373 13425 Z= 0.281 Chirality : 0.042 0.210 1474 Planarity : 0.004 0.045 1744 Dihedral : 7.786 151.632 1463 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.43 % Allowed : 16.21 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.25), residues: 1211 helix: 1.82 (0.24), residues: 496 sheet: 0.34 (0.35), residues: 230 loop : -1.14 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 254 TYR 0.045 0.001 TYR K 54 PHE 0.010 0.001 PHE K 303 TRP 0.016 0.001 TRP A 21 HIS 0.002 0.000 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9894) covalent geometry : angle 0.56913 (13425) hydrogen bonds : bond 0.03362 ( 455) hydrogen bonds : angle 4.03631 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2314.13 seconds wall clock time: 40 minutes 30.85 seconds (2430.85 seconds total)