Starting phenix.real_space_refine on Fri Sep 11 14:07:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nbh_0411/09_2026/6nbh_0411.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbh_0411/09_2026/6nbh_0411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nbh_0411/09_2026/6nbh_0411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbh_0411/09_2026/6nbh_0411.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nbh_0411/09_2026/6nbh_0411.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nbh_0411/09_2026/6nbh_0411.cif" model { file = "/net/cci-nas-00/data/ceres_data/6nbh_0411/09_2026/6nbh_0411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbh_0411/09_2026/6nbh_0411.cif" } resolution = 3.5 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= -0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 6121 2.51 5 N 1627 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9502 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3098 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 11, 'TRANS': 367} Chain breaks: 3 Chain: "P" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 283 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1873 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 250 Unusual residues: {'CLR': 7, 'PLM': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 2.03, per 1000 atoms: 0.21 Number of scatterers: 9502 At special positions: 0 Unit cell: (125.736, 99.372, 150.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1697 8.00 N 1627 7.00 C 6121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.04 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 0.80 Conformation dependent library (CDL) restraints added in 322.9 milliseconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 41.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 33 through 56 removed outlier: 3.534A pdb=" N GLN R 37 " --> pdb=" O THR R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.793A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET R 189 " --> pdb=" O ASP R 185 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE R 190 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU R 199 " --> pdb=" O TYR R 195 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU R 202 " --> pdb=" O SER R 198 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL R 206 " --> pdb=" O LEU R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 239 removed outlier: 3.815A pdb=" N ILE R 222 " --> pdb=" O THR R 218 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS R 223 " --> pdb=" O ARG R 219 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET R 224 " --> pdb=" O ASN R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 250 removed outlier: 4.265A pdb=" N VAL R 243 " --> pdb=" O VAL R 239 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU R 244 " --> pdb=" O LYS R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 278 Processing helix chain 'R' and resid 279 through 312 removed outlier: 3.521A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU R 292 " --> pdb=" O PHE R 288 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE R 311 " --> pdb=" O HIS R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.612A pdb=" N THR R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL R 326 " --> pdb=" O TRP R 322 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE R 327 " --> pdb=" O GLY R 323 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.725A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 369 removed outlier: 3.502A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 371 through 381 removed outlier: 3.633A pdb=" N ILE R 381 " --> pdb=" O LEU R 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 391 removed outlier: 3.651A pdb=" N THR R 387 " --> pdb=" O ARG R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 412 Processing helix chain 'R' and resid 413 through 418 removed outlier: 3.552A pdb=" N PHE R 417 " --> pdb=" O LEU R 413 " (cutoff:3.500A) Processing helix chain 'R' and resid 419 through 424 Processing helix chain 'R' and resid 434 through 460 removed outlier: 3.514A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR R 459 " --> pdb=" O VAL R 455 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing helix chain 'P' and resid 2 through 32 removed outlier: 3.720A pdb=" N ARG P 20 " --> pdb=" O GLN P 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.735A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.727A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.616A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.583A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.707A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.844A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.638A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 126 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 213 removed outlier: 4.326A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.002A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.229A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.568A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.520A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.772A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.483A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.518A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.566A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 4.108A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1209 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: 1.25 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3015 1.35 - 1.47: 2338 1.47 - 1.59: 4290 1.59 - 1.71: 0 1.71 - 1.83: 80 Bond restraints: 9723 Sorted by residual: bond pdb=" N HIS R 114 " pdb=" CA HIS R 114 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.54e+00 bond pdb=" C MET R 414 " pdb=" N PRO R 415 " ideal model delta sigma weight residual 1.335 1.364 -0.028 1.36e-02 5.41e+03 4.30e+00 bond pdb=" C THR A 320 " pdb=" N PRO A 321 " ideal model delta sigma weight residual 1.331 1.356 -0.025 1.20e-02 6.94e+03 4.20e+00 bond pdb=" C ASP G 48 " pdb=" N PRO G 49 " ideal model delta sigma weight residual 1.332 1.348 -0.016 8.90e-03 1.26e+04 3.12e+00 bond pdb=" C LEU R 331 " pdb=" N PRO R 332 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.28e-02 6.10e+03 2.42e+00 ... (remaining 9718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 11821 1.37 - 2.75: 1232 2.75 - 4.12: 116 4.12 - 5.50: 18 5.50 - 6.87: 2 Bond angle restraints: 13189 Sorted by residual: angle pdb=" CA ASP A 354 " pdb=" CB ASP A 354 " pdb=" CG ASP A 354 " ideal model delta sigma weight residual 112.60 116.94 -4.34 1.00e+00 1.00e+00 1.89e+01 angle pdb=" N VAL R 382 " pdb=" CA VAL R 382 " pdb=" C VAL R 382 " ideal model delta sigma weight residual 112.43 108.49 3.94 9.20e-01 1.18e+00 1.84e+01 angle pdb=" C LYS N 76 " pdb=" N ASN N 77 " pdb=" CA ASN N 77 " ideal model delta sigma weight residual 122.07 126.86 -4.79 1.43e+00 4.89e-01 1.12e+01 angle pdb=" N PRO B 236 " pdb=" CA PRO B 236 " pdb=" C PRO B 236 " ideal model delta sigma weight residual 112.47 119.34 -6.87 2.06e+00 2.36e-01 1.11e+01 angle pdb=" CA ASN N 77 " pdb=" CB ASN N 77 " pdb=" CG ASN N 77 " ideal model delta sigma weight residual 112.60 115.91 -3.31 1.00e+00 1.00e+00 1.10e+01 ... (remaining 13184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.71: 5436 13.71 - 27.43: 207 27.43 - 41.14: 51 41.14 - 54.85: 9 54.85 - 68.57: 3 Dihedral angle restraints: 5706 sinusoidal: 2336 harmonic: 3370 Sorted by residual: dihedral pdb=" CA ILE R 381 " pdb=" C ILE R 381 " pdb=" N VAL R 382 " pdb=" CA VAL R 382 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 128.88 -35.88 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CA LEU R 202 " pdb=" C LEU R 202 " pdb=" N THR R 203 " pdb=" CA THR R 203 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 5703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1025 0.052 - 0.104: 364 0.104 - 0.157: 67 0.157 - 0.209: 14 0.209 - 0.261: 3 Chirality restraints: 1473 Sorted by residual: chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C14 CLR R 603 " pdb=" C13 CLR R 603 " pdb=" C15 CLR R 603 " pdb=" C8 CLR R 603 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1470 not shown) Planarity restraints: 1633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.030 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO G 49 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 414 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO R 415 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 415 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 415 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 376 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C PHE A 376 " -0.021 2.00e-02 2.50e+03 pdb=" O PHE A 376 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN A 377 " 0.007 2.00e-02 2.50e+03 ... (remaining 1630 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 3045 2.87 - 3.37: 8150 3.37 - 3.88: 14781 3.88 - 4.39: 16289 4.39 - 4.90: 28764 Nonbonded interactions: 71029 Sorted by model distance: nonbonded pdb=" OH TYR A 360 " pdb=" OD2 ASP A 381 " model vdw 2.357 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.390 3.040 nonbonded pdb=" O ARG A 42 " pdb=" OG1 THR A 242 " model vdw 2.399 3.040 nonbonded pdb=" O VAL R 412 " pdb=" OH TYR R 459 " model vdw 2.400 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.407 3.040 ... (remaining 71024 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 group one per residue 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: 1.010 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.830 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.005 0.028 9729 Z= 0.359 Angle : 0.867 6.871 13201 Z= 0.567 Chirality : 0.054 0.261 1473 Planarity : 0.003 0.046 1633 Dihedral : 8.344 68.568 3508 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.20 % Allowed : 0.71 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.22), residues: 1135 helix: -0.27 (0.22), residues: 446 sheet: -0.70 (0.33), residues: 210 loop : -1.78 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.016 0.002 TYR N 80 PHE 0.013 0.002 PHE R 138 TRP 0.015 0.002 TRP R 437 HIS 0.009 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.36 ( 9723) covalent geometry : angle 0.86491 / 0.57 (13189) SS BOND : bond 0.00540 / 0.25 ( 6) SS BOND : angle 2.09711 / 0.97 ( 12) hydrogen bonds : bond 0.14799 / 10.07 ( 421) hydrogen bonds : angle 6.99698 / 4.94 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 444 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.7194 (mtp) cc_final: 0.6646 (ppp) REVERT: R 348 ASN cc_start: 0.6392 (t0) cc_final: 0.6170 (t0) REVERT: R 404 ARG cc_start: 0.7618 (mtt180) cc_final: 0.6903 (tpt170) REVERT: R 408 LYS cc_start: 0.8141 (tttt) cc_final: 0.7918 (tttm) REVERT: R 433 SER cc_start: 0.7747 (t) cc_final: 0.7401 (p) REVERT: R 474 TRP cc_start: 0.6368 (t60) cc_final: 0.5924 (t60) REVERT: A 31 GLN cc_start: 0.8784 (mm-40) cc_final: 0.7642 (tm-30) REVERT: B 65 THR cc_start: 0.8859 (p) cc_final: 0.8609 (t) REVERT: B 123 ILE cc_start: 0.8181 (mt) cc_final: 0.7959 (mt) REVERT: B 184 THR cc_start: 0.8151 (p) cc_final: 0.7920 (t) REVERT: B 303 ASP cc_start: 0.9190 (t70) cc_final: 0.8772 (p0) REVERT: N 29 PHE cc_start: 0.8684 (t80) cc_final: 0.8321 (t80) REVERT: N 31 ASN cc_start: 0.8484 (m-40) cc_final: 0.8279 (t0) REVERT: N 57 SER cc_start: 0.9014 (t) cc_final: 0.8761 (m) REVERT: N 68 PHE cc_start: 0.7194 (m-10) cc_final: 0.6686 (m-10) REVERT: N 93 VAL cc_start: 0.8190 (t) cc_final: 0.7810 (p) REVERT: N 124 VAL cc_start: 0.8660 (t) cc_final: 0.8449 (m) outliers start: 2 outliers final: 1 residues processed: 445 average time/residue: 0.1026 time to fit residues: 61.1437 Evaluate side-chains 247 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0040 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 47 GLN R 140 HIS R 295 ASN R 364 GLN R 451 GLN P 32 HIS A 23 ASN A 271 ASN B 88 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.160550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.119296 restraints weight = 15757.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.123853 restraints weight = 7234.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126922 restraints weight = 4539.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128873 restraints weight = 3408.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.129816 restraints weight = 2847.049| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9729 Z= 0.129 Angle : 0.607 8.955 13201 Z= 0.319 Chirality : 0.042 0.206 1473 Planarity : 0.005 0.055 1633 Dihedral : 4.990 45.470 1376 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.34 % Allowed : 14.88 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1135 helix: 1.31 (0.25), residues: 440 sheet: -0.30 (0.33), residues: 216 loop : -1.15 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 214 TYR 0.015 0.001 TYR R 191 PHE 0.021 0.002 PHE B 235 TRP 0.028 0.002 TRP R 298 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9723) covalent geometry : angle 0.60632 / 0.32 (13189) SS BOND : bond 0.00254 / 0.12 ( 6) SS BOND : angle 1.07898 / 0.55 ( 12) hydrogen bonds : bond 0.04273 / 2.89 ( 421) hydrogen bonds : angle 4.81637 / 3.47 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 216 HIS cc_start: 0.7677 (m90) cc_final: 0.6984 (m170) REVERT: R 404 ARG cc_start: 0.7440 (mtt180) cc_final: 0.7025 (tpt170) REVERT: R 408 LYS cc_start: 0.7976 (tttt) cc_final: 0.7732 (tttm) REVERT: R 438 GLN cc_start: 0.7751 (mt0) cc_final: 0.7536 (mt0) REVERT: R 457 ILE cc_start: 0.8919 (tp) cc_final: 0.8710 (tp) REVERT: R 474 TRP cc_start: 0.5875 (t60) cc_final: 0.5591 (t60) REVERT: A 19 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8677 (mt0) REVERT: A 31 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8031 (tm-30) REVERT: A 310 ASP cc_start: 0.8329 (p0) cc_final: 0.7944 (p0) REVERT: A 315 PHE cc_start: 0.7328 (t80) cc_final: 0.7128 (t80) REVERT: B 127 LYS cc_start: 0.8531 (mmmt) cc_final: 0.7870 (mttp) REVERT: B 138 GLU cc_start: 0.8099 (pp20) cc_final: 0.7815 (pp20) REVERT: B 169 TRP cc_start: 0.8649 (m100) cc_final: 0.8434 (m100) REVERT: B 175 GLN cc_start: 0.8392 (tt0) cc_final: 0.7884 (tm-30) REVERT: B 235 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8361 (t80) REVERT: B 298 ASP cc_start: 0.8648 (t0) cc_final: 0.8071 (p0) REVERT: B 303 ASP cc_start: 0.8444 (t70) cc_final: 0.7537 (p0) REVERT: N 31 ASN cc_start: 0.8675 (m-40) cc_final: 0.8353 (t0) REVERT: N 38 ARG cc_start: 0.7184 (ptt90) cc_final: 0.6791 (ptm-80) REVERT: N 57 SER cc_start: 0.8637 (t) cc_final: 0.8422 (m) REVERT: N 65 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7663 (tppt) REVERT: N 98 ARG cc_start: 0.8777 (ttp80) cc_final: 0.7870 (tmm-80) outliers start: 33 outliers final: 20 residues processed: 283 average time/residue: 0.0986 time to fit residues: 38.3171 Evaluate side-chains 238 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain P residue 23 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 84 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 295 ASN B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.152067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110225 restraints weight = 15982.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.114489 restraints weight = 7535.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.117313 restraints weight = 4832.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.119070 restraints weight = 3685.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120215 restraints weight = 3135.902| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9729 Z= 0.173 Angle : 0.615 6.873 13201 Z= 0.321 Chirality : 0.042 0.165 1473 Planarity : 0.004 0.045 1633 Dihedral : 5.086 44.462 1376 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.67 % Allowed : 15.89 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1135 helix: 1.66 (0.25), residues: 442 sheet: 0.22 (0.33), residues: 213 loop : -0.89 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.020 0.002 TYR R 191 PHE 0.023 0.002 PHE B 235 TRP 0.024 0.002 TRP R 298 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9723) covalent geometry : angle 0.61459 / 0.32 (13189) SS BOND : bond 0.00658 / 0.46 ( 6) SS BOND : angle 1.08485 / 0.64 ( 12) hydrogen bonds : bond 0.04101 / 2.85 ( 421) hydrogen bonds : angle 4.42960 / 3.19 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.4952 (ttp) cc_final: 0.4002 (ttt) REVERT: R 216 HIS cc_start: 0.8371 (m90) cc_final: 0.8108 (m90) REVERT: R 309 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8375 (tp) REVERT: R 352 TRP cc_start: 0.8910 (m-10) cc_final: 0.8620 (m-90) REVERT: R 404 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7108 (tpt170) REVERT: R 411 LEU cc_start: 0.8793 (mt) cc_final: 0.8062 (tt) REVERT: R 445 MET cc_start: 0.8241 (mmm) cc_final: 0.7948 (mmp) REVERT: R 455 VAL cc_start: 0.7741 (OUTLIER) cc_final: 0.7480 (t) REVERT: R 457 ILE cc_start: 0.9066 (tp) cc_final: 0.8839 (tp) REVERT: R 474 TRP cc_start: 0.5921 (t60) cc_final: 0.5642 (t60) REVERT: A 19 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8695 (mt0) REVERT: A 31 GLN cc_start: 0.8884 (mm-40) cc_final: 0.7998 (tm-30) REVERT: A 229 ASP cc_start: 0.8140 (m-30) cc_final: 0.7489 (p0) REVERT: A 310 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8169 (p0) REVERT: A 344 GLU cc_start: 0.8236 (tp30) cc_final: 0.8034 (tp30) REVERT: A 379 CYS cc_start: 0.8323 (t) cc_final: 0.7982 (t) REVERT: B 120 ILE cc_start: 0.8551 (mt) cc_final: 0.8295 (mm) REVERT: B 138 GLU cc_start: 0.8140 (pp20) cc_final: 0.7827 (pp20) REVERT: B 165 THR cc_start: 0.8218 (p) cc_final: 0.7951 (p) REVERT: B 175 GLN cc_start: 0.8451 (tt0) cc_final: 0.7965 (tm-30) REVERT: B 215 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8235 (mp0) REVERT: B 235 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8223 (t80) REVERT: B 312 ASP cc_start: 0.6705 (p0) cc_final: 0.6337 (p0) REVERT: B 339 TRP cc_start: 0.8638 (m100) cc_final: 0.8194 (m100) REVERT: N 28 THR cc_start: 0.8768 (t) cc_final: 0.8542 (t) REVERT: N 31 ASN cc_start: 0.8922 (m-40) cc_final: 0.8306 (t0) REVERT: N 34 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7565 (mtm) REVERT: N 38 ARG cc_start: 0.7530 (ptt90) cc_final: 0.7161 (ptm-80) REVERT: N 43 LYS cc_start: 0.6998 (mmmt) cc_final: 0.6763 (mmmt) REVERT: N 65 LYS cc_start: 0.8301 (ttmm) cc_final: 0.8023 (tppt) REVERT: N 91 THR cc_start: 0.7387 (OUTLIER) cc_final: 0.7155 (t) REVERT: N 93 VAL cc_start: 0.7934 (t) cc_final: 0.7722 (p) outliers start: 56 outliers final: 32 residues processed: 283 average time/residue: 0.0846 time to fit residues: 33.8177 Evaluate side-chains 256 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 455 VAL Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 23 PHE Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 0.0030 chunk 15 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 77 optimal weight: 0.0980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.155707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113831 restraints weight = 16009.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.118364 restraints weight = 7315.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.121407 restraints weight = 4598.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123334 restraints weight = 3458.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.124515 restraints weight = 2908.762| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 9729 Z= 0.109 Angle : 0.556 9.730 13201 Z= 0.289 Chirality : 0.040 0.159 1473 Planarity : 0.004 0.048 1633 Dihedral : 4.544 33.839 1375 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.85 % Allowed : 20.34 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1135 helix: 1.94 (0.25), residues: 440 sheet: 0.39 (0.34), residues: 208 loop : -0.85 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.016 0.001 TYR A 391 PHE 0.024 0.001 PHE R 327 TRP 0.018 0.001 TRP R 298 HIS 0.004 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9723) covalent geometry : angle 0.55586 / 0.29 (13189) SS BOND : bond 0.00295 / 0.15 ( 6) SS BOND : angle 0.68486 / 0.44 ( 12) hydrogen bonds : bond 0.03466 / 2.41 ( 421) hydrogen bonds : angle 4.19110 / 3.00 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.4233 (ttp) cc_final: 0.3971 (tpp) REVERT: R 134 TYR cc_start: 0.7040 (p90) cc_final: 0.6836 (p90) REVERT: R 216 HIS cc_start: 0.8446 (m90) cc_final: 0.8138 (m90) REVERT: R 309 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8315 (tp) REVERT: R 321 LEU cc_start: 0.8573 (tp) cc_final: 0.8110 (tt) REVERT: R 404 ARG cc_start: 0.7445 (mtt180) cc_final: 0.7127 (tpt170) REVERT: R 408 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8149 (tptt) REVERT: R 411 LEU cc_start: 0.8818 (mt) cc_final: 0.8037 (tt) REVERT: R 445 MET cc_start: 0.8278 (mmm) cc_final: 0.7875 (mmp) REVERT: R 457 ILE cc_start: 0.9005 (tp) cc_final: 0.8776 (tp) REVERT: R 474 TRP cc_start: 0.5893 (t60) cc_final: 0.5569 (t60) REVERT: A 19 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8682 (mt0) REVERT: A 31 GLN cc_start: 0.8844 (mm-40) cc_final: 0.7980 (tm-30) REVERT: A 268 GLU cc_start: 0.8221 (tm-30) cc_final: 0.8017 (tp30) REVERT: A 310 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8192 (p0) REVERT: A 379 CYS cc_start: 0.8208 (t) cc_final: 0.7893 (t) REVERT: A 392 GLU cc_start: 0.7216 (tt0) cc_final: 0.6639 (tm-30) REVERT: B 120 ILE cc_start: 0.8487 (mt) cc_final: 0.8257 (mm) REVERT: B 138 GLU cc_start: 0.8140 (pp20) cc_final: 0.7842 (pp20) REVERT: B 148 CYS cc_start: 0.9123 (t) cc_final: 0.8730 (t) REVERT: B 169 TRP cc_start: 0.8655 (m100) cc_final: 0.8069 (m100) REVERT: B 175 GLN cc_start: 0.8401 (tt0) cc_final: 0.8043 (tm-30) REVERT: B 235 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8175 (t80) REVERT: B 273 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 334 SER cc_start: 0.8852 (m) cc_final: 0.8287 (t) REVERT: G 51 LEU cc_start: 0.7465 (mm) cc_final: 0.7185 (mm) REVERT: N 31 ASN cc_start: 0.8881 (m-40) cc_final: 0.8165 (t0) REVERT: N 34 MET cc_start: 0.7836 (mtp) cc_final: 0.7532 (mtp) REVERT: N 38 ARG cc_start: 0.7543 (ptt90) cc_final: 0.7227 (ptm-80) REVERT: N 65 LYS cc_start: 0.8330 (ttmm) cc_final: 0.8043 (tppt) REVERT: N 93 VAL cc_start: 0.8068 (t) cc_final: 0.7786 (p) REVERT: N 98 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8482 (tmm-80) outliers start: 38 outliers final: 24 residues processed: 265 average time/residue: 0.0973 time to fit residues: 36.1874 Evaluate side-chains 235 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 223 HIS R 295 ASN R 402 GLN A 14 ASN B 75 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.149362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107336 restraints weight = 16199.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111566 restraints weight = 7650.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114341 restraints weight = 4906.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116146 restraints weight = 3757.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.117213 restraints weight = 3194.675| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9729 Z= 0.185 Angle : 0.619 6.937 13201 Z= 0.324 Chirality : 0.043 0.174 1473 Planarity : 0.004 0.054 1633 Dihedral : 4.866 33.734 1375 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.55 % Allowed : 20.85 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1135 helix: 1.81 (0.25), residues: 448 sheet: 0.47 (0.34), residues: 217 loop : -0.76 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 214 TYR 0.022 0.002 TYR R 191 PHE 0.023 0.002 PHE B 235 TRP 0.038 0.002 TRP R 352 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 9723) covalent geometry : angle 0.61833 / 0.32 (13189) SS BOND : bond 0.00365 / 0.17 ( 6) SS BOND : angle 1.15040 / 0.64 ( 12) hydrogen bonds : bond 0.03906 / 2.69 ( 421) hydrogen bonds : angle 4.24975 / 3.04 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.4906 (ttp) cc_final: 0.4297 (ttt) REVERT: R 134 TYR cc_start: 0.7301 (p90) cc_final: 0.7097 (p90) REVERT: R 309 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8293 (tp) REVERT: R 404 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7321 (tpt170) REVERT: R 411 LEU cc_start: 0.8890 (mt) cc_final: 0.8123 (tt) REVERT: R 445 MET cc_start: 0.8202 (mmm) cc_final: 0.7974 (mmp) REVERT: R 474 TRP cc_start: 0.5969 (t60) cc_final: 0.5742 (t60) REVERT: A 19 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8686 (mt0) REVERT: A 31 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8065 (tm-30) REVERT: A 229 ASP cc_start: 0.8238 (m-30) cc_final: 0.7689 (p0) REVERT: A 379 CYS cc_start: 0.8402 (t) cc_final: 0.8036 (t) REVERT: A 392 GLU cc_start: 0.7211 (tt0) cc_final: 0.6623 (tm-30) REVERT: B 58 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8876 (mp) REVERT: B 120 ILE cc_start: 0.8597 (mt) cc_final: 0.8280 (mm) REVERT: B 138 GLU cc_start: 0.8186 (pp20) cc_final: 0.7897 (pp20) REVERT: B 175 GLN cc_start: 0.8397 (tt0) cc_final: 0.7913 (tm-30) REVERT: B 235 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8105 (t80) REVERT: B 273 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8480 (mp) REVERT: B 334 SER cc_start: 0.8973 (m) cc_final: 0.8489 (t) REVERT: G 48 ASP cc_start: 0.8271 (p0) cc_final: 0.7752 (p0) REVERT: N 31 ASN cc_start: 0.9045 (m110) cc_final: 0.8131 (t0) REVERT: N 34 MET cc_start: 0.7864 (mtp) cc_final: 0.7435 (mtm) REVERT: N 38 ARG cc_start: 0.7669 (ptt90) cc_final: 0.7138 (ptm-80) REVERT: N 68 PHE cc_start: 0.8140 (m-10) cc_final: 0.7587 (m-10) REVERT: N 93 VAL cc_start: 0.8071 (t) cc_final: 0.7850 (p) outliers start: 45 outliers final: 35 residues processed: 252 average time/residue: 0.0920 time to fit residues: 32.4757 Evaluate side-chains 252 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 410 THR Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 46 optimal weight: 0.3980 chunk 95 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 402 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.150170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.108892 restraints weight = 16015.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113180 restraints weight = 7363.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.116047 restraints weight = 4668.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.117866 restraints weight = 3542.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.118801 restraints weight = 3006.838| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9729 Z= 0.132 Angle : 0.582 7.362 13201 Z= 0.302 Chirality : 0.041 0.159 1473 Planarity : 0.004 0.069 1633 Dihedral : 4.632 35.773 1375 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.55 % Allowed : 21.96 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1135 helix: 1.97 (0.25), residues: 445 sheet: 0.64 (0.35), residues: 216 loop : -0.76 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.017 0.001 TYR R 191 PHE 0.023 0.001 PHE B 235 TRP 0.018 0.001 TRP N 47 HIS 0.004 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9723) covalent geometry : angle 0.58113 / 0.30 (13189) SS BOND : bond 0.00249 / 0.11 ( 6) SS BOND : angle 0.97904 / 0.56 ( 12) hydrogen bonds : bond 0.03495 / 2.43 ( 421) hydrogen bonds : angle 4.13867 / 2.95 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.4898 (ttp) cc_final: 0.4226 (ttt) REVERT: R 216 HIS cc_start: 0.8438 (m90) cc_final: 0.8015 (m90) REVERT: R 309 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8305 (tp) REVERT: R 353 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8275 (t0) REVERT: R 380 ASN cc_start: 0.9014 (t0) cc_final: 0.8399 (t0) REVERT: R 404 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7270 (tpt170) REVERT: R 411 LEU cc_start: 0.8916 (mt) cc_final: 0.8186 (tt) REVERT: R 445 MET cc_start: 0.8139 (mmm) cc_final: 0.7747 (mmp) REVERT: R 474 TRP cc_start: 0.5934 (t60) cc_final: 0.5685 (t60) REVERT: P 16 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8656 (mm-40) REVERT: A 19 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8577 (tt0) REVERT: A 31 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8127 (tm-30) REVERT: A 229 ASP cc_start: 0.8123 (m-30) cc_final: 0.7664 (p0) REVERT: A 244 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7636 (mt) REVERT: A 379 CYS cc_start: 0.8361 (t) cc_final: 0.8045 (t) REVERT: A 392 GLU cc_start: 0.6985 (tt0) cc_final: 0.6578 (tp30) REVERT: B 58 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8755 (mp) REVERT: B 120 ILE cc_start: 0.8585 (mt) cc_final: 0.8263 (mm) REVERT: B 138 GLU cc_start: 0.8236 (pp20) cc_final: 0.7934 (pp20) REVERT: B 169 TRP cc_start: 0.8733 (m100) cc_final: 0.8222 (m100) REVERT: B 175 GLN cc_start: 0.8421 (tt0) cc_final: 0.8045 (tm-30) REVERT: B 235 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8056 (t80) REVERT: B 273 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8400 (mp) REVERT: B 334 SER cc_start: 0.8913 (m) cc_final: 0.8354 (t) REVERT: N 31 ASN cc_start: 0.9135 (m110) cc_final: 0.8200 (t0) REVERT: N 34 MET cc_start: 0.7799 (mtp) cc_final: 0.7576 (mtt) REVERT: N 38 ARG cc_start: 0.7771 (ptt90) cc_final: 0.7240 (ptm-80) REVERT: N 93 VAL cc_start: 0.8155 (t) cc_final: 0.7929 (p) REVERT: N 104 THR cc_start: 0.8241 (t) cc_final: 0.7919 (t) outliers start: 45 outliers final: 29 residues processed: 255 average time/residue: 0.0935 time to fit residues: 33.5339 Evaluate side-chains 239 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 410 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 77 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 13 optimal weight: 0.0980 chunk 106 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 402 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.151780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110139 restraints weight = 15879.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114584 restraints weight = 7225.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.117523 restraints weight = 4556.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.119371 restraints weight = 3451.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.120432 restraints weight = 2925.549| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9729 Z= 0.118 Angle : 0.582 7.934 13201 Z= 0.304 Chirality : 0.041 0.182 1473 Planarity : 0.004 0.071 1633 Dihedral : 4.490 36.063 1375 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.15 % Allowed : 22.87 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1135 helix: 2.04 (0.25), residues: 445 sheet: 0.70 (0.35), residues: 218 loop : -0.65 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 214 TYR 0.024 0.001 TYR R 134 PHE 0.023 0.001 PHE B 235 TRP 0.016 0.001 TRP N 47 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9723) covalent geometry : angle 0.58184 / 0.30 (13189) SS BOND : bond 0.00219 / 0.11 ( 6) SS BOND : angle 0.97305 / 0.54 ( 12) hydrogen bonds : bond 0.03378 / 2.28 ( 421) hydrogen bonds : angle 4.11789 / 2.95 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8294 (tp) REVERT: R 353 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8029 (t0) REVERT: R 404 ARG cc_start: 0.7719 (mtt180) cc_final: 0.7336 (tpt170) REVERT: R 411 LEU cc_start: 0.8786 (mt) cc_final: 0.8092 (tt) REVERT: R 445 MET cc_start: 0.8144 (mmm) cc_final: 0.7720 (mmp) REVERT: R 474 TRP cc_start: 0.5866 (t60) cc_final: 0.5626 (t60) REVERT: P 20 ARG cc_start: 0.9032 (tmm-80) cc_final: 0.8449 (tmm-80) REVERT: A 19 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8557 (tt0) REVERT: A 31 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8204 (tm-30) REVERT: A 58 LYS cc_start: 0.7557 (tmtt) cc_final: 0.7132 (mtpp) REVERT: A 229 ASP cc_start: 0.8192 (m-30) cc_final: 0.7832 (p0) REVERT: A 244 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7582 (mt) REVERT: A 379 CYS cc_start: 0.8315 (t) cc_final: 0.8028 (t) REVERT: A 386 MET cc_start: 0.8117 (ttm) cc_final: 0.7882 (tmm) REVERT: A 392 GLU cc_start: 0.7052 (tt0) cc_final: 0.6667 (tp30) REVERT: B 58 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8723 (mp) REVERT: B 111 TYR cc_start: 0.8841 (m-10) cc_final: 0.8437 (m-80) REVERT: B 138 GLU cc_start: 0.8266 (pp20) cc_final: 0.8030 (pp20) REVERT: B 148 CYS cc_start: 0.9190 (t) cc_final: 0.8683 (t) REVERT: B 169 TRP cc_start: 0.8663 (m100) cc_final: 0.8105 (m100) REVERT: B 175 GLN cc_start: 0.8419 (tt0) cc_final: 0.8024 (tm-30) REVERT: B 235 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8005 (t80) REVERT: B 273 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8321 (mp) REVERT: B 334 SER cc_start: 0.8886 (m) cc_final: 0.8325 (t) REVERT: G 21 MET cc_start: 0.7189 (mmm) cc_final: 0.6749 (mmt) REVERT: N 31 ASN cc_start: 0.9155 (m110) cc_final: 0.8226 (t0) REVERT: N 34 MET cc_start: 0.7781 (mtp) cc_final: 0.7422 (mtt) REVERT: N 38 ARG cc_start: 0.7367 (ptt90) cc_final: 0.7027 (ptm-80) REVERT: N 58 ILE cc_start: 0.8475 (mt) cc_final: 0.8273 (mt) REVERT: N 93 VAL cc_start: 0.8179 (t) cc_final: 0.7964 (p) REVERT: N 104 THR cc_start: 0.8124 (t) cc_final: 0.7771 (t) outliers start: 41 outliers final: 29 residues processed: 247 average time/residue: 0.0945 time to fit residues: 32.8033 Evaluate side-chains 241 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 410 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.0040 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 17 optimal weight: 0.0010 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 402 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.153125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.112038 restraints weight = 15941.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116565 restraints weight = 7200.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.119590 restraints weight = 4489.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121510 restraints weight = 3373.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122541 restraints weight = 2835.357| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9729 Z= 0.113 Angle : 0.586 8.257 13201 Z= 0.305 Chirality : 0.040 0.157 1473 Planarity : 0.004 0.067 1633 Dihedral : 4.380 35.841 1375 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.64 % Allowed : 23.99 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.13 (0.26), residues: 1135 helix: 2.11 (0.25), residues: 440 sheet: 0.84 (0.35), residues: 212 loop : -0.58 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.021 0.001 TYR R 134 PHE 0.023 0.001 PHE B 235 TRP 0.017 0.001 TRP N 47 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 9723) covalent geometry : angle 0.58518 / 0.31 (13189) SS BOND : bond 0.00210 / 0.10 ( 6) SS BOND : angle 0.89135 / 0.50 ( 12) hydrogen bonds : bond 0.03275 / 2.24 ( 421) hydrogen bonds : angle 4.04773 / 2.89 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5008 (ppp) REVERT: R 216 HIS cc_start: 0.8500 (m90) cc_final: 0.8121 (m90) REVERT: R 309 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8293 (tp) REVERT: R 353 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.7997 (t0) REVERT: R 404 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7306 (tpt170) REVERT: R 411 LEU cc_start: 0.8659 (mt) cc_final: 0.8067 (tt) REVERT: R 445 MET cc_start: 0.8153 (mmm) cc_final: 0.7771 (mmp) REVERT: R 474 TRP cc_start: 0.5882 (t60) cc_final: 0.5633 (t60) REVERT: A 19 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8570 (tt0) REVERT: A 31 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8221 (tm-30) REVERT: A 58 LYS cc_start: 0.7526 (tmtt) cc_final: 0.7169 (mtpp) REVERT: A 229 ASP cc_start: 0.8195 (m-30) cc_final: 0.7897 (p0) REVERT: A 244 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7631 (mt) REVERT: A 386 MET cc_start: 0.8102 (ttm) cc_final: 0.7893 (tmm) REVERT: A 392 GLU cc_start: 0.7075 (tt0) cc_final: 0.6769 (tp30) REVERT: B 111 TYR cc_start: 0.8813 (m-10) cc_final: 0.8468 (m-80) REVERT: B 138 GLU cc_start: 0.8224 (pp20) cc_final: 0.7947 (pp20) REVERT: B 148 CYS cc_start: 0.9167 (t) cc_final: 0.8663 (t) REVERT: B 163 ASP cc_start: 0.7607 (p0) cc_final: 0.7060 (p0) REVERT: B 169 TRP cc_start: 0.8643 (m100) cc_final: 0.8078 (m100) REVERT: B 175 GLN cc_start: 0.8324 (tt0) cc_final: 0.7992 (tm-30) REVERT: B 235 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8022 (t80) REVERT: B 246 ASP cc_start: 0.8399 (m-30) cc_final: 0.8046 (m-30) REVERT: B 334 SER cc_start: 0.8867 (m) cc_final: 0.8350 (t) REVERT: G 21 MET cc_start: 0.7152 (mmm) cc_final: 0.6564 (mmt) REVERT: N 31 ASN cc_start: 0.9148 (m110) cc_final: 0.8267 (t0) REVERT: N 34 MET cc_start: 0.7739 (mtp) cc_final: 0.7455 (mtt) REVERT: N 53 GLN cc_start: 0.8001 (mp10) cc_final: 0.7505 (mp10) REVERT: N 58 ILE cc_start: 0.8472 (mt) cc_final: 0.8258 (mt) REVERT: N 93 VAL cc_start: 0.8263 (t) cc_final: 0.8053 (p) REVERT: N 104 THR cc_start: 0.7986 (t) cc_final: 0.7724 (t) outliers start: 36 outliers final: 25 residues processed: 243 average time/residue: 0.0934 time to fit residues: 31.9917 Evaluate side-chains 238 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 402 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN N 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.151070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110042 restraints weight = 15937.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114438 restraints weight = 7251.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117361 restraints weight = 4545.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119219 restraints weight = 3425.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.120232 restraints weight = 2885.880| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9729 Z= 0.139 Angle : 0.614 8.400 13201 Z= 0.320 Chirality : 0.042 0.171 1473 Planarity : 0.004 0.067 1633 Dihedral : 4.518 36.495 1375 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.85 % Allowed : 23.38 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1135 helix: 2.11 (0.25), residues: 440 sheet: 0.72 (0.35), residues: 218 loop : -0.53 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 214 TYR 0.020 0.001 TYR R 134 PHE 0.027 0.001 PHE N 27 TRP 0.016 0.001 TRP N 47 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9723) covalent geometry : angle 0.61343 / 0.32 (13189) SS BOND : bond 0.00467 / 0.18 ( 6) SS BOND : angle 1.12675 / 0.58 ( 12) hydrogen bonds : bond 0.03450 / 2.32 ( 421) hydrogen bonds : angle 4.02935 / 2.84 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.5882 (ptp) cc_final: 0.5069 (ppp) REVERT: R 216 HIS cc_start: 0.8477 (m90) cc_final: 0.8061 (m90) REVERT: R 309 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8324 (tp) REVERT: R 353 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8115 (t0) REVERT: R 404 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7335 (tpt170) REVERT: R 410 THR cc_start: 0.9102 (m) cc_final: 0.8827 (t) REVERT: R 411 LEU cc_start: 0.8658 (mt) cc_final: 0.8109 (tt) REVERT: R 445 MET cc_start: 0.8179 (mmm) cc_final: 0.7818 (mmp) REVERT: R 474 TRP cc_start: 0.5870 (t60) cc_final: 0.5609 (t60) REVERT: P 20 ARG cc_start: 0.8967 (tmm-80) cc_final: 0.8474 (ptt-90) REVERT: A 19 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8582 (tt0) REVERT: A 31 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8236 (tm-30) REVERT: A 58 LYS cc_start: 0.7470 (tmtt) cc_final: 0.7165 (mtpp) REVERT: A 229 ASP cc_start: 0.8259 (m-30) cc_final: 0.7939 (p0) REVERT: A 244 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7629 (mt) REVERT: A 386 MET cc_start: 0.8127 (ttm) cc_final: 0.7918 (tmm) REVERT: A 392 GLU cc_start: 0.7153 (tt0) cc_final: 0.6779 (tp30) REVERT: B 58 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8759 (mp) REVERT: B 111 TYR cc_start: 0.8894 (m-10) cc_final: 0.8537 (m-80) REVERT: B 138 GLU cc_start: 0.8238 (pp20) cc_final: 0.7945 (pp20) REVERT: B 163 ASP cc_start: 0.7636 (p0) cc_final: 0.7131 (p0) REVERT: B 169 TRP cc_start: 0.8728 (m100) cc_final: 0.8192 (m100) REVERT: B 175 GLN cc_start: 0.8317 (tt0) cc_final: 0.7969 (tm-30) REVERT: B 235 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8044 (t80) REVERT: B 246 ASP cc_start: 0.8356 (m-30) cc_final: 0.8025 (m-30) REVERT: B 273 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8097 (mp) REVERT: B 334 SER cc_start: 0.8888 (m) cc_final: 0.8374 (t) REVERT: G 27 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7579 (mpt180) REVERT: N 34 MET cc_start: 0.7789 (mtp) cc_final: 0.7493 (mtt) REVERT: N 58 ILE cc_start: 0.8523 (mt) cc_final: 0.8313 (mt) REVERT: N 90 ASP cc_start: 0.7898 (m-30) cc_final: 0.7664 (m-30) REVERT: N 93 VAL cc_start: 0.8223 (t) cc_final: 0.8021 (p) REVERT: N 104 THR cc_start: 0.8033 (t) cc_final: 0.7699 (t) outliers start: 38 outliers final: 30 residues processed: 238 average time/residue: 0.0906 time to fit residues: 30.7837 Evaluate side-chains 239 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 402 GLN R 448 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN N 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.149699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108941 restraints weight = 15856.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113291 restraints weight = 7226.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116144 restraints weight = 4533.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.118004 restraints weight = 3420.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119075 restraints weight = 2887.385| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9729 Z= 0.151 Angle : 0.644 12.104 13201 Z= 0.331 Chirality : 0.042 0.161 1473 Planarity : 0.004 0.067 1633 Dihedral : 4.630 37.901 1375 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.44 % Allowed : 24.29 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.08 (0.26), residues: 1135 helix: 2.06 (0.25), residues: 440 sheet: 0.70 (0.34), residues: 220 loop : -0.54 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 214 TYR 0.021 0.001 TYR R 134 PHE 0.025 0.002 PHE N 27 TRP 0.021 0.001 TRP N 47 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9723) covalent geometry : angle 0.64382 / 0.33 (13189) SS BOND : bond 0.00308 / 0.13 ( 6) SS BOND : angle 1.10155 / 0.58 ( 12) hydrogen bonds : bond 0.03500 / 2.35 ( 421) hydrogen bonds : angle 4.11798 / 2.88 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.5943 (ptp) cc_final: 0.5126 (ppp) REVERT: R 309 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8311 (tp) REVERT: R 353 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8065 (t0) REVERT: R 404 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7308 (tpt170) REVERT: R 411 LEU cc_start: 0.8717 (mt) cc_final: 0.8204 (tt) REVERT: R 445 MET cc_start: 0.8184 (mmm) cc_final: 0.7823 (mmp) REVERT: R 474 TRP cc_start: 0.5924 (t60) cc_final: 0.5642 (t60) REVERT: P 20 ARG cc_start: 0.8988 (tmm-80) cc_final: 0.8553 (ptt-90) REVERT: A 19 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8563 (tt0) REVERT: A 31 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8242 (tm-30) REVERT: A 58 LYS cc_start: 0.7538 (tmtt) cc_final: 0.7201 (mtpp) REVERT: A 229 ASP cc_start: 0.8262 (m-30) cc_final: 0.7983 (p0) REVERT: A 244 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7610 (mt) REVERT: A 349 SER cc_start: 0.9136 (t) cc_final: 0.8914 (p) REVERT: A 386 MET cc_start: 0.8129 (ttm) cc_final: 0.7913 (tmm) REVERT: A 392 GLU cc_start: 0.7233 (tt0) cc_final: 0.6773 (tp30) REVERT: B 58 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8762 (mp) REVERT: B 138 GLU cc_start: 0.8247 (pp20) cc_final: 0.7948 (pp20) REVERT: B 163 ASP cc_start: 0.7671 (p0) cc_final: 0.7313 (p0) REVERT: B 169 TRP cc_start: 0.8746 (m100) cc_final: 0.8225 (m100) REVERT: B 175 GLN cc_start: 0.8312 (tt0) cc_final: 0.7992 (tm-30) REVERT: B 235 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8022 (t80) REVERT: B 246 ASP cc_start: 0.8322 (m-30) cc_final: 0.7992 (m-30) REVERT: B 254 ASP cc_start: 0.7785 (t0) cc_final: 0.7467 (t0) REVERT: B 270 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8556 (tp) REVERT: B 273 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8061 (mp) REVERT: B 334 SER cc_start: 0.8905 (m) cc_final: 0.8393 (t) REVERT: G 21 MET cc_start: 0.6879 (mmm) cc_final: 0.6368 (mmt) REVERT: G 27 ARG cc_start: 0.7848 (mtt90) cc_final: 0.7283 (mpt180) REVERT: N 34 MET cc_start: 0.7801 (mtp) cc_final: 0.7570 (mtt) REVERT: N 53 GLN cc_start: 0.8038 (mp10) cc_final: 0.7561 (mp10) REVERT: N 80 TYR cc_start: 0.7165 (m-80) cc_final: 0.6877 (m-80) REVERT: N 90 ASP cc_start: 0.7631 (m-30) cc_final: 0.7169 (m-30) REVERT: N 104 THR cc_start: 0.7906 (t) cc_final: 0.7645 (t) outliers start: 34 outliers final: 26 residues processed: 234 average time/residue: 0.0955 time to fit residues: 31.6373 Evaluate side-chains 232 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 0.3980 chunk 95 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 402 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.149876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.108816 restraints weight = 15953.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113178 restraints weight = 7293.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.116072 restraints weight = 4597.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.117851 restraints weight = 3479.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.118830 restraints weight = 2947.362| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9729 Z= 0.145 Angle : 0.678 19.331 13201 Z= 0.340 Chirality : 0.043 0.307 1473 Planarity : 0.004 0.066 1633 Dihedral : 4.687 39.135 1375 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.64 % Allowed : 24.39 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.26), residues: 1135 helix: 2.00 (0.25), residues: 440 sheet: 0.64 (0.34), residues: 220 loop : -0.52 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.020 0.001 TYR R 134 PHE 0.026 0.002 PHE N 27 TRP 0.031 0.001 TRP N 47 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 9723) covalent geometry : angle 0.67785 / 0.34 (13189) SS BOND : bond 0.00311 / 0.14 ( 6) SS BOND : angle 1.06607 / 0.57 ( 12) hydrogen bonds : bond 0.03501 / 2.37 ( 421) hydrogen bonds : angle 4.10250 / 2.86 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.76 seconds wall clock time: 35 minutes 40.51 seconds (2140.51 seconds total)