Starting phenix.real_space_refine on Wed Mar 4 01:05:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nbh_0411/03_2026/6nbh_0411.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbh_0411/03_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_0411/03_2026/6nbh_0411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbh_0411/03_2026/6nbh_0411.map" model { file = "/net/cci-nas-00/data/ceres_data/6nbh_0411/03_2026/6nbh_0411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbh_0411/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.18, per 1000 atoms: 0.23 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: 0.73 Conformation dependent library (CDL) restraints added in 339.5 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: 0.31 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: 1.43 Time building geometry restraints manager: 1.01 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: 5792 13.71 - 27.43: 233 27.43 - 41.14: 59 41.14 - 54.85: 11 54.85 - 68.57: 3 Dihedral angle restraints: 6098 sinusoidal: 2728 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 6095 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 8.431 68.568 3900 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 covalent geometry : bond 0.00526 ( 9723) covalent geometry : angle 0.86491 (13189) SS BOND : bond 0.00540 ( 6) SS BOND : angle 2.09711 ( 12) hydrogen bonds : bond 0.14799 ( 421) hydrogen bonds : angle 6.99698 ( 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 : 0.383 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: 0.1072 time to fit residues: 63.0669 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 : 0.274 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.160506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.119345 restraints weight = 15751.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123862 restraints weight = 7287.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126919 restraints weight = 4596.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128817 restraints weight = 3452.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.129742 restraints weight = 2897.036| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9729 Z= 0.127 Angle : 0.604 8.782 13201 Z= 0.318 Chirality : 0.043 0.208 1473 Planarity : 0.005 0.055 1633 Dihedral : 5.741 45.412 1768 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.54 % Allowed : 14.68 % 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: -0.04 (0.24), residues: 1135 helix: 1.31 (0.25), residues: 440 sheet: -0.31 (0.33), residues: 216 loop : -1.14 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.015 0.001 TYR R 191 PHE 0.020 0.002 PHE B 235 TRP 0.029 0.001 TRP R 298 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9723) covalent geometry : angle 0.60352 (13189) SS BOND : bond 0.00285 ( 6) SS BOND : angle 1.06782 ( 12) hydrogen bonds : bond 0.04270 ( 421) hydrogen bonds : angle 4.80827 ( 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 297 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 216 HIS cc_start: 0.7666 (m90) cc_final: 0.6986 (m170) REVERT: R 404 ARG cc_start: 0.7434 (mtt180) cc_final: 0.7036 (tpt170) REVERT: R 408 LYS cc_start: 0.7998 (tttt) cc_final: 0.7752 (tttm) REVERT: R 422 ILE cc_start: 0.9496 (tp) cc_final: 0.9289 (tp) REVERT: R 438 GLN cc_start: 0.7749 (mt0) cc_final: 0.7523 (mt0) REVERT: R 457 ILE cc_start: 0.8936 (tp) cc_final: 0.8725 (tp) REVERT: R 474 TRP cc_start: 0.5858 (t60) cc_final: 0.5582 (t60) REVERT: P 17 ASP cc_start: 0.8465 (t70) cc_final: 0.8206 (t70) REVERT: A 19 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8684 (mt0) REVERT: A 31 GLN cc_start: 0.9010 (mm-40) cc_final: 0.7998 (tm-30) REVERT: A 250 SER cc_start: 0.7657 (t) cc_final: 0.7366 (t) REVERT: A 315 PHE cc_start: 0.7359 (t80) cc_final: 0.7132 (t80) REVERT: A 318 TYR cc_start: 0.6753 (t80) cc_final: 0.6539 (t80) REVERT: B 127 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7868 (mttp) REVERT: B 138 GLU cc_start: 0.8099 (pp20) cc_final: 0.7821 (pp20) REVERT: B 169 TRP cc_start: 0.8650 (m100) cc_final: 0.8441 (m100) REVERT: B 175 GLN cc_start: 0.8386 (tt0) cc_final: 0.7881 (tm-30) REVERT: B 235 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8311 (t80) REVERT: B 298 ASP cc_start: 0.8615 (t0) cc_final: 0.8080 (p0) REVERT: B 303 ASP cc_start: 0.8445 (t70) cc_final: 0.7653 (p0) REVERT: N 31 ASN cc_start: 0.8700 (m-40) cc_final: 0.8396 (t0) REVERT: N 38 ARG cc_start: 0.7245 (ptt90) cc_final: 0.6921 (ptm-80) REVERT: N 57 SER cc_start: 0.8659 (t) cc_final: 0.8443 (m) REVERT: N 65 LYS cc_start: 0.7924 (ttmm) cc_final: 0.7672 (tppt) REVERT: N 80 TYR cc_start: 0.7330 (m-80) cc_final: 0.7104 (m-80) outliers start: 35 outliers final: 21 residues processed: 286 average time/residue: 0.0980 time to fit residues: 38.1576 Evaluate side-chains 241 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 157 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: 7.9990 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN A 59 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 = 0.4036 r_free = 0.4036 target = 0.151455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109749 restraints weight = 16033.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113958 restraints weight = 7552.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116693 restraints weight = 4843.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118481 restraints weight = 3708.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.119421 restraints weight = 3151.479| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9729 Z= 0.182 Angle : 0.617 6.791 13201 Z= 0.324 Chirality : 0.043 0.179 1473 Planarity : 0.004 0.048 1633 Dihedral : 5.761 44.586 1768 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.77 % Allowed : 16.40 % Favored : 77.83 % 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: 0.47 (0.25), residues: 1135 helix: 1.62 (0.25), residues: 442 sheet: 0.21 (0.33), residues: 214 loop : -0.87 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 214 TYR 0.021 0.002 TYR R 191 PHE 0.023 0.002 PHE B 235 TRP 0.024 0.002 TRP R 298 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9723) covalent geometry : angle 0.61586 (13189) SS BOND : bond 0.00803 ( 6) SS BOND : angle 1.12048 ( 12) hydrogen bonds : bond 0.04174 ( 421) hydrogen bonds : angle 4.44054 ( 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: 57 poor density : 243 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.5007 (ttp) cc_final: 0.3994 (ttt) REVERT: R 309 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8372 (tp) REVERT: R 352 TRP cc_start: 0.8877 (m-10) cc_final: 0.8587 (m-90) REVERT: R 404 ARG cc_start: 0.7504 (mtt180) cc_final: 0.7190 (tpt170) REVERT: R 411 LEU cc_start: 0.8800 (mt) cc_final: 0.8065 (tt) REVERT: R 445 MET cc_start: 0.8224 (mmm) cc_final: 0.7933 (mmp) REVERT: R 455 VAL cc_start: 0.7724 (OUTLIER) cc_final: 0.6895 (m) REVERT: R 457 ILE cc_start: 0.9054 (tp) cc_final: 0.8841 (tp) REVERT: R 474 TRP cc_start: 0.5912 (t60) cc_final: 0.5612 (t60) REVERT: P 10 GLN cc_start: 0.8983 (mm110) cc_final: 0.8692 (mm110) REVERT: A 19 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8690 (mt0) REVERT: A 31 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8001 (tm-30) REVERT: A 229 ASP cc_start: 0.8162 (m-30) cc_final: 0.7501 (p0) REVERT: A 379 CYS cc_start: 0.8357 (t) cc_final: 0.8008 (t) REVERT: B 120 ILE cc_start: 0.8546 (mt) cc_final: 0.8291 (mm) REVERT: B 138 GLU cc_start: 0.8129 (pp20) cc_final: 0.7849 (pp20) REVERT: B 175 GLN cc_start: 0.8454 (tt0) cc_final: 0.7964 (tm-30) REVERT: B 214 ARG cc_start: 0.8013 (mtm110) cc_final: 0.7739 (mtm110) REVERT: B 215 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8239 (mp0) REVERT: B 235 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8171 (t80) REVERT: B 312 ASP cc_start: 0.6522 (p0) cc_final: 0.6309 (p0) REVERT: N 28 THR cc_start: 0.8767 (t) cc_final: 0.8533 (t) REVERT: N 31 ASN cc_start: 0.8975 (m-40) cc_final: 0.8290 (t0) REVERT: N 34 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7489 (mtm) REVERT: N 38 ARG cc_start: 0.7550 (ptt90) cc_final: 0.7112 (ptm-80) REVERT: N 47 TRP cc_start: 0.7189 (t60) cc_final: 0.6904 (t60) REVERT: N 65 LYS cc_start: 0.8359 (ttmm) cc_final: 0.8091 (tppt) REVERT: N 80 TYR cc_start: 0.7269 (m-80) cc_final: 0.6908 (m-80) REVERT: N 91 THR cc_start: 0.7407 (OUTLIER) cc_final: 0.7174 (t) REVERT: N 93 VAL cc_start: 0.7926 (t) cc_final: 0.7715 (p) outliers start: 57 outliers final: 34 residues processed: 282 average time/residue: 0.0897 time to fit residues: 35.4104 Evaluate side-chains 253 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 15 ILE 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 380 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER 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: 0.0980 chunk 15 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 HIS A 59 GLN B 88 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.154952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113129 restraints weight = 16025.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.117586 restraints weight = 7403.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120550 restraints weight = 4689.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122441 restraints weight = 3557.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123527 restraints weight = 3007.032| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9729 Z= 0.111 Angle : 0.547 6.444 13201 Z= 0.289 Chirality : 0.041 0.158 1473 Planarity : 0.004 0.047 1633 Dihedral : 5.178 33.345 1767 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.74 % Allowed : 19.74 % Favored : 76.52 % 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: 0.68 (0.25), residues: 1135 helix: 1.85 (0.25), residues: 442 sheet: 0.33 (0.34), residues: 212 loop : -0.82 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 22 TYR 0.017 0.001 TYR A 391 PHE 0.024 0.001 PHE R 327 TRP 0.017 0.001 TRP R 298 HIS 0.004 0.001 HIS R 114 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9723) covalent geometry : angle 0.54710 (13189) SS BOND : bond 0.00280 ( 6) SS BOND : angle 0.65394 ( 12) hydrogen bonds : bond 0.03504 ( 421) hydrogen bonds : angle 4.19723 ( 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 280 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.4402 (ttp) cc_final: 0.3967 (tpp) REVERT: R 216 HIS cc_start: 0.8310 (m90) cc_final: 0.7886 (m90) REVERT: R 309 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8322 (tp) REVERT: R 321 LEU cc_start: 0.8607 (tp) cc_final: 0.8143 (tt) REVERT: R 352 TRP cc_start: 0.8822 (m-10) cc_final: 0.8584 (m-90) REVERT: R 404 ARG cc_start: 0.7457 (mtt180) cc_final: 0.7146 (tpt170) REVERT: R 408 LYS cc_start: 0.8438 (ttpt) cc_final: 0.8153 (tptt) REVERT: R 411 LEU cc_start: 0.8828 (mt) cc_final: 0.8042 (tt) REVERT: R 445 MET cc_start: 0.8284 (mmm) cc_final: 0.7880 (mmp) REVERT: R 457 ILE cc_start: 0.9004 (tp) cc_final: 0.8794 (tp) REVERT: R 474 TRP cc_start: 0.5884 (t60) cc_final: 0.5528 (t60) REVERT: A 19 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8687 (mt0) REVERT: A 31 GLN cc_start: 0.8847 (mm-40) cc_final: 0.7985 (tm-30) REVERT: A 51 SER cc_start: 0.6799 (m) cc_final: 0.6586 (p) REVERT: A 244 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7596 (mt) REVERT: A 268 GLU cc_start: 0.8225 (tm-30) cc_final: 0.8023 (tp30) REVERT: A 379 CYS cc_start: 0.8201 (t) cc_final: 0.7895 (t) REVERT: A 392 GLU cc_start: 0.7184 (tt0) cc_final: 0.6632 (tm-30) REVERT: B 120 ILE cc_start: 0.8501 (mt) cc_final: 0.8267 (mm) REVERT: B 138 GLU cc_start: 0.8155 (pp20) cc_final: 0.7865 (pp20) REVERT: B 148 CYS cc_start: 0.9279 (t) cc_final: 0.8735 (t) REVERT: B 169 TRP cc_start: 0.8635 (m100) cc_final: 0.8141 (m100) REVERT: B 175 GLN cc_start: 0.8402 (tt0) cc_final: 0.8036 (tm-30) REVERT: B 235 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8193 (t80) REVERT: B 273 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 334 SER cc_start: 0.8867 (m) cc_final: 0.8326 (t) REVERT: G 51 LEU cc_start: 0.7482 (mm) cc_final: 0.7198 (mm) REVERT: N 31 ASN cc_start: 0.8958 (m-40) cc_final: 0.8192 (t0) REVERT: N 34 MET cc_start: 0.7830 (mtp) cc_final: 0.7539 (mtp) REVERT: N 38 ARG cc_start: 0.7549 (ptt90) cc_final: 0.7150 (ptm-80) REVERT: N 47 TRP cc_start: 0.6988 (t60) cc_final: 0.6719 (t60) REVERT: N 65 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8089 (tppt) REVERT: N 80 TYR cc_start: 0.7278 (m-80) cc_final: 0.6870 (m-80) REVERT: N 91 THR cc_start: 0.7312 (OUTLIER) cc_final: 0.7101 (t) REVERT: N 93 VAL cc_start: 0.8097 (t) cc_final: 0.7827 (p) outliers start: 37 outliers final: 23 residues processed: 271 average time/residue: 0.0900 time to fit residues: 34.3400 Evaluate side-chains 239 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 86 LEU Chi-restraints excluded: chain N residue 91 THR 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: 7.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN R 402 GLN A 14 ASN A 59 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.146583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104575 restraints weight = 16262.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108730 restraints weight = 7625.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111416 restraints weight = 4885.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113196 restraints weight = 3746.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114287 restraints weight = 3188.406| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9729 Z= 0.221 Angle : 0.661 6.815 13201 Z= 0.346 Chirality : 0.045 0.189 1473 Planarity : 0.004 0.052 1633 Dihedral : 5.780 36.331 1767 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.77 % Allowed : 20.04 % Favored : 74.19 % 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: 0.59 (0.25), residues: 1135 helix: 1.56 (0.24), residues: 448 sheet: 0.34 (0.34), residues: 226 loop : -0.72 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 214 TYR 0.026 0.002 TYR R 191 PHE 0.023 0.002 PHE B 235 TRP 0.016 0.002 TRP A 281 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 9723) covalent geometry : angle 0.66006 (13189) SS BOND : bond 0.00459 ( 6) SS BOND : angle 1.18885 ( 12) hydrogen bonds : bond 0.04231 ( 421) hydrogen bonds : angle 4.38247 ( 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 277 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 THR cc_start: 0.8764 (p) cc_final: 0.8531 (t) REVERT: R 309 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8271 (tp) REVERT: R 404 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7283 (tpt170) REVERT: R 411 LEU cc_start: 0.8982 (mt) cc_final: 0.8205 (tt) REVERT: R 445 MET cc_start: 0.8289 (mmm) cc_final: 0.8070 (mmp) REVERT: R 474 TRP cc_start: 0.6070 (t60) cc_final: 0.5792 (t60) REVERT: P 20 ARG cc_start: 0.9003 (tmm-80) cc_final: 0.8668 (ttp80) REVERT: A 19 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8718 (mt0) REVERT: A 31 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8116 (tm-30) REVERT: A 229 ASP cc_start: 0.8244 (m-30) cc_final: 0.7760 (p0) REVERT: A 267 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8269 (tp-100) REVERT: A 379 CYS cc_start: 0.8482 (t) cc_final: 0.8062 (t) REVERT: A 392 GLU cc_start: 0.7252 (tt0) cc_final: 0.6635 (tm-30) REVERT: B 58 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8878 (mp) REVERT: B 138 GLU cc_start: 0.8262 (pp20) cc_final: 0.8001 (pp20) REVERT: B 175 GLN cc_start: 0.8412 (tt0) cc_final: 0.7899 (tm-30) REVERT: B 235 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8155 (t80) REVERT: B 273 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8451 (mp) REVERT: B 334 SER cc_start: 0.8978 (m) cc_final: 0.8544 (t) REVERT: N 34 MET cc_start: 0.7857 (mtp) cc_final: 0.7448 (mtt) REVERT: N 38 ARG cc_start: 0.7698 (ptt90) cc_final: 0.6987 (ptm-80) REVERT: N 65 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8391 (tppt) REVERT: N 80 TYR cc_start: 0.7616 (m-80) cc_final: 0.7182 (m-80) REVERT: N 93 VAL cc_start: 0.8181 (t) cc_final: 0.7915 (p) outliers start: 57 outliers final: 41 residues processed: 262 average time/residue: 0.0958 time to fit residues: 35.0275 Evaluate side-chains 246 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain R residue 283 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 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 409 SER Chi-restraints excluded: chain R residue 410 THR Chi-restraints excluded: chain P residue 23 PHE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 221 MET 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 276 ILE Chi-restraints excluded: chain A residue 284 THR 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 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 300 LEU 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 86 LEU 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: 9.9990 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN R 402 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.149326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108211 restraints weight = 16038.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112528 restraints weight = 7249.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.115409 restraints weight = 4553.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117171 restraints weight = 3449.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118288 restraints weight = 2925.759| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9729 Z= 0.131 Angle : 0.598 7.864 13201 Z= 0.311 Chirality : 0.041 0.158 1473 Planarity : 0.004 0.062 1633 Dihedral : 5.214 38.291 1767 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.05 % Allowed : 22.17 % Favored : 73.79 % 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: 0.74 (0.25), residues: 1135 helix: 1.78 (0.25), residues: 445 sheet: 0.48 (0.34), residues: 215 loop : -0.73 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.017 0.001 TYR R 134 PHE 0.023 0.002 PHE B 235 TRP 0.016 0.001 TRP R 298 HIS 0.004 0.001 HIS R 114 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9723) covalent geometry : angle 0.59786 (13189) SS BOND : bond 0.00250 ( 6) SS BOND : angle 0.93131 ( 12) hydrogen bonds : bond 0.03576 ( 421) hydrogen bonds : angle 4.21523 ( 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 257 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8279 (tp) REVERT: R 352 TRP cc_start: 0.8800 (m-10) cc_final: 0.8397 (m-90) REVERT: R 353 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8244 (t0) REVERT: R 404 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7314 (tpt170) REVERT: R 410 THR cc_start: 0.9070 (m) cc_final: 0.8808 (t) REVERT: R 411 LEU cc_start: 0.8849 (mt) cc_final: 0.8218 (tt) REVERT: R 445 MET cc_start: 0.8147 (mmm) cc_final: 0.7744 (mmp) REVERT: R 474 TRP cc_start: 0.5953 (t60) cc_final: 0.5648 (t60) REVERT: P 16 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8714 (mm-40) REVERT: P 20 ARG cc_start: 0.8833 (tmm-80) cc_final: 0.8537 (ttp80) REVERT: A 19 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8566 (tt0) REVERT: A 31 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8153 (tm-30) REVERT: A 229 ASP cc_start: 0.8190 (m-30) cc_final: 0.7808 (p0) REVERT: A 244 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7586 (mt) REVERT: A 379 CYS cc_start: 0.8376 (t) cc_final: 0.8032 (t) REVERT: A 392 GLU cc_start: 0.7029 (tt0) cc_final: 0.6636 (tm-30) REVERT: B 58 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8711 (mp) REVERT: B 138 GLU cc_start: 0.8252 (pp20) cc_final: 0.7986 (pp20) REVERT: B 169 TRP cc_start: 0.8761 (m100) cc_final: 0.8206 (m100) REVERT: B 175 GLN cc_start: 0.8378 (tt0) cc_final: 0.8009 (tm-30) REVERT: B 196 THR cc_start: 0.9199 (m) cc_final: 0.8992 (p) REVERT: B 235 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7964 (t80) REVERT: B 273 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8356 (mp) REVERT: B 334 SER cc_start: 0.8921 (m) cc_final: 0.8383 (t) REVERT: G 27 ARG cc_start: 0.7791 (mtt90) cc_final: 0.7303 (mpt-90) REVERT: N 34 MET cc_start: 0.7781 (mtp) cc_final: 0.7487 (mtp) REVERT: N 38 ARG cc_start: 0.7463 (ptt90) cc_final: 0.7070 (ptm-80) REVERT: N 65 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8411 (tppt) REVERT: N 80 TYR cc_start: 0.7804 (m-80) cc_final: 0.7429 (m-80) REVERT: N 104 THR cc_start: 0.8171 (t) cc_final: 0.7829 (t) outliers start: 40 outliers final: 25 residues processed: 245 average time/residue: 0.0915 time to fit residues: 31.4898 Evaluate side-chains 232 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 286 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 40.0000 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 402 GLN R 448 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.150386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109560 restraints weight = 15882.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.113886 restraints weight = 7260.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116758 restraints weight = 4575.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118447 restraints weight = 3466.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.119631 restraints weight = 2951.847| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.6316 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= 0.124 Angle : 0.595 7.985 13201 Z= 0.309 Chirality : 0.041 0.173 1473 Planarity : 0.004 0.065 1633 Dihedral : 5.135 38.880 1767 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.74 % Allowed : 23.28 % 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: 0.84 (0.25), residues: 1135 helix: 1.89 (0.25), residues: 442 sheet: 0.60 (0.34), residues: 218 loop : -0.74 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 214 TYR 0.019 0.001 TYR R 134 PHE 0.025 0.001 PHE N 68 TRP 0.013 0.001 TRP R 298 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9723) covalent geometry : angle 0.59380 (13189) SS BOND : bond 0.00243 ( 6) SS BOND : angle 1.17367 ( 12) hydrogen bonds : bond 0.03502 ( 421) hydrogen bonds : angle 4.14541 ( 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 255 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8318 (tp) REVERT: R 352 TRP cc_start: 0.8731 (m-10) cc_final: 0.8393 (m-90) REVERT: R 353 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8151 (t0) REVERT: R 404 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7367 (tpt170) REVERT: R 410 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8854 (t) REVERT: R 411 LEU cc_start: 0.8815 (mt) cc_final: 0.8176 (tt) REVERT: R 445 MET cc_start: 0.8126 (mmm) cc_final: 0.7717 (mmp) REVERT: R 474 TRP cc_start: 0.5996 (t60) cc_final: 0.5665 (t60) REVERT: A 31 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8182 (tm-30) REVERT: A 229 ASP cc_start: 0.8203 (m-30) cc_final: 0.7864 (p0) REVERT: A 244 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7722 (mt) REVERT: A 379 CYS cc_start: 0.8330 (t) cc_final: 0.8019 (t) REVERT: A 392 GLU cc_start: 0.7011 (tt0) cc_final: 0.6591 (tp30) REVERT: B 58 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8749 (mp) REVERT: B 138 GLU cc_start: 0.8250 (pp20) cc_final: 0.8003 (pp20) REVERT: B 148 CYS cc_start: 0.9167 (t) cc_final: 0.8692 (t) REVERT: B 163 ASP cc_start: 0.7735 (p0) cc_final: 0.7317 (p0) REVERT: B 169 TRP cc_start: 0.8690 (m100) cc_final: 0.8152 (m100) REVERT: B 175 GLN cc_start: 0.8395 (tt0) cc_final: 0.8038 (tm-30) REVERT: B 196 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8960 (p) REVERT: B 235 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8062 (t80) REVERT: B 273 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8306 (mp) REVERT: B 334 SER cc_start: 0.8914 (m) cc_final: 0.8398 (t) REVERT: G 21 MET cc_start: 0.7242 (mmm) cc_final: 0.6652 (mmt) REVERT: G 27 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7511 (mpt-90) REVERT: N 34 MET cc_start: 0.7766 (mtp) cc_final: 0.7494 (mtm) REVERT: N 38 ARG cc_start: 0.7553 (ptt90) cc_final: 0.7130 (ptm-80) REVERT: N 65 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8409 (tppt) REVERT: N 80 TYR cc_start: 0.7657 (m-80) cc_final: 0.7273 (m-80) REVERT: N 104 THR cc_start: 0.8017 (t) cc_final: 0.7649 (t) outliers start: 37 outliers final: 27 residues processed: 244 average time/residue: 0.0863 time to fit residues: 29.6959 Evaluate side-chains 240 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 196 THR 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 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: 4.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 50.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN R 402 GLN ** B 340 ASN ** 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 = 0.3997 r_free = 0.3997 target = 0.147483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106460 restraints weight = 16047.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110617 restraints weight = 7404.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.113375 restraints weight = 4718.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.115096 restraints weight = 3607.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.115991 restraints weight = 3072.224| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.6567 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= 0.168 Angle : 0.633 8.100 13201 Z= 0.329 Chirality : 0.043 0.176 1473 Planarity : 0.004 0.064 1633 Dihedral : 5.316 40.602 1767 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.66 % Allowed : 23.08 % 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: 0.80 (0.25), residues: 1135 helix: 1.79 (0.25), residues: 446 sheet: 0.37 (0.33), residues: 235 loop : -0.62 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 214 TYR 0.019 0.001 TYR R 191 PHE 0.024 0.002 PHE N 27 TRP 0.011 0.001 TRP R 298 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9723) covalent geometry : angle 0.63213 (13189) SS BOND : bond 0.00364 ( 6) SS BOND : angle 1.10555 ( 12) hydrogen bonds : bond 0.03778 ( 421) hydrogen bonds : angle 4.14680 ( 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 251 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8307 (tp) REVERT: R 353 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8322 (t0) REVERT: R 404 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7278 (tpt170) REVERT: R 411 LEU cc_start: 0.8930 (mt) cc_final: 0.8313 (tt) REVERT: R 445 MET cc_start: 0.8147 (mmm) cc_final: 0.7789 (mmp) REVERT: R 474 TRP cc_start: 0.6002 (t60) cc_final: 0.5690 (t60) REVERT: P 20 ARG cc_start: 0.8872 (ttp80) cc_final: 0.8356 (ttp80) REVERT: A 31 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8195 (tm-30) REVERT: A 229 ASP cc_start: 0.8273 (m-30) cc_final: 0.7955 (p0) REVERT: A 244 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7703 (mt) REVERT: A 349 SER cc_start: 0.9201 (t) cc_final: 0.8956 (p) REVERT: A 379 CYS cc_start: 0.8328 (t) cc_final: 0.7999 (t) REVERT: A 392 GLU cc_start: 0.7095 (tt0) cc_final: 0.6683 (tp30) REVERT: B 58 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8873 (mp) REVERT: B 138 GLU cc_start: 0.8243 (pp20) cc_final: 0.7923 (pp20) REVERT: B 163 ASP cc_start: 0.7774 (p0) cc_final: 0.7443 (p0) REVERT: B 169 TRP cc_start: 0.8806 (m100) cc_final: 0.8397 (m100) REVERT: B 175 GLN cc_start: 0.8351 (tt0) cc_final: 0.7991 (tm-30) REVERT: B 235 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8083 (t80) REVERT: B 270 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8497 (tp) REVERT: B 273 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8264 (mp) REVERT: B 334 SER cc_start: 0.8944 (m) cc_final: 0.8467 (t) REVERT: G 58 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8228 (mm-30) REVERT: N 34 MET cc_start: 0.7781 (mtp) cc_final: 0.7553 (mtm) REVERT: N 38 ARG cc_start: 0.7579 (ptt90) cc_final: 0.6963 (ptm-80) REVERT: N 65 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8617 (tppt) REVERT: N 80 TYR cc_start: 0.7657 (m-80) cc_final: 0.7277 (m-80) REVERT: N 104 THR cc_start: 0.7950 (t) cc_final: 0.7599 (t) outliers start: 46 outliers final: 31 residues processed: 237 average time/residue: 0.0924 time to fit residues: 30.8925 Evaluate side-chains 235 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 413 LEU 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 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 200 VAL Chi-restraints excluded: chain B residue 205 ASP 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 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 Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4014 r_free = 0.4014 target = 0.148808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.107881 restraints weight = 15986.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112149 restraints weight = 7281.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.114936 restraints weight = 4594.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.116677 restraints weight = 3491.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117721 restraints weight = 2968.705| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9729 Z= 0.138 Angle : 0.644 10.198 13201 Z= 0.329 Chirality : 0.042 0.157 1473 Planarity : 0.004 0.062 1633 Dihedral : 5.186 41.855 1767 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.05 % Allowed : 23.89 % Favored : 72.06 % 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: 0.78 (0.26), residues: 1135 helix: 1.81 (0.25), residues: 442 sheet: 0.45 (0.33), residues: 224 loop : -0.68 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 214 TYR 0.016 0.001 TYR R 278 PHE 0.023 0.001 PHE B 235 TRP 0.013 0.001 TRP R 298 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9723) covalent geometry : angle 0.64255 (13189) SS BOND : bond 0.00343 ( 6) SS BOND : angle 1.60172 ( 12) hydrogen bonds : bond 0.03567 ( 421) hydrogen bonds : angle 4.15027 ( 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 248 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8324 (tp) REVERT: R 353 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8164 (t0) REVERT: R 404 ARG cc_start: 0.7410 (mtt180) cc_final: 0.7171 (tpt170) REVERT: R 411 LEU cc_start: 0.8911 (mt) cc_final: 0.8285 (tt) REVERT: R 427 THR cc_start: 0.8530 (m) cc_final: 0.7917 (p) REVERT: R 445 MET cc_start: 0.8197 (mmm) cc_final: 0.7788 (mmp) REVERT: R 474 TRP cc_start: 0.6049 (t60) cc_final: 0.5695 (t60) REVERT: P 20 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8519 (ptt-90) REVERT: A 31 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8209 (tm-30) REVERT: A 229 ASP cc_start: 0.8262 (m-30) cc_final: 0.7952 (p0) REVERT: A 244 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7720 (mt) REVERT: A 349 SER cc_start: 0.9167 (t) cc_final: 0.8931 (p) REVERT: A 379 CYS cc_start: 0.8353 (t) cc_final: 0.8040 (t) REVERT: A 392 GLU cc_start: 0.7119 (tt0) cc_final: 0.6673 (tp30) REVERT: B 58 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8803 (mp) REVERT: B 138 GLU cc_start: 0.8243 (pp20) cc_final: 0.7925 (pp20) REVERT: B 163 ASP cc_start: 0.7759 (p0) cc_final: 0.7445 (p0) REVERT: B 169 TRP cc_start: 0.8751 (m100) cc_final: 0.8343 (m100) REVERT: B 175 GLN cc_start: 0.8316 (tt0) cc_final: 0.7979 (tm-30) REVERT: B 235 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8048 (t80) REVERT: B 254 ASP cc_start: 0.7783 (t0) cc_final: 0.7475 (t0) REVERT: B 270 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8554 (tp) REVERT: B 273 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8189 (mp) REVERT: B 297 TRP cc_start: 0.9225 (m100) cc_final: 0.9017 (m100) REVERT: B 333 ASP cc_start: 0.7694 (t0) cc_final: 0.7425 (t0) REVERT: B 334 SER cc_start: 0.8931 (m) cc_final: 0.8448 (t) REVERT: G 21 MET cc_start: 0.7005 (mmm) cc_final: 0.6486 (mmt) REVERT: G 27 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7187 (mpt180) REVERT: G 58 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8253 (mm-30) REVERT: N 34 MET cc_start: 0.7797 (mtp) cc_final: 0.7473 (mtt) REVERT: N 38 ARG cc_start: 0.7349 (ptt90) cc_final: 0.7108 (ptm-80) REVERT: N 58 ILE cc_start: 0.8485 (mt) cc_final: 0.8230 (mt) REVERT: N 65 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8636 (tppt) REVERT: N 80 TYR cc_start: 0.7762 (m-80) cc_final: 0.7274 (m-80) REVERT: N 104 THR cc_start: 0.7810 (t) cc_final: 0.7455 (t) outliers start: 40 outliers final: 30 residues processed: 236 average time/residue: 0.0989 time to fit residues: 32.8305 Evaluate side-chains 234 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 353 ASP Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 440 GLN 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 157 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 205 ASP 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 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 122 THR 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: 0.8980 chunk 50 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 88 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN R 402 GLN A 267 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.150408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110195 restraints weight = 15785.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.114490 restraints weight = 7149.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.117271 restraints weight = 4483.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.119063 restraints weight = 3398.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120065 restraints weight = 2876.699| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.6779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9729 Z= 0.124 Angle : 0.642 10.791 13201 Z= 0.325 Chirality : 0.041 0.157 1473 Planarity : 0.004 0.061 1633 Dihedral : 5.022 42.728 1767 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.44 % Allowed : 24.90 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.26), residues: 1135 helix: 1.90 (0.25), residues: 439 sheet: 0.55 (0.33), residues: 223 loop : -0.62 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 214 TYR 0.013 0.001 TYR R 191 PHE 0.023 0.001 PHE R 291 TRP 0.013 0.001 TRP R 298 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9723) covalent geometry : angle 0.64109 (13189) SS BOND : bond 0.00351 ( 6) SS BOND : angle 1.25723 ( 12) hydrogen bonds : bond 0.03471 ( 421) hydrogen bonds : angle 4.17172 ( 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 247 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8333 (tp) REVERT: R 353 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8253 (t70) REVERT: R 404 ARG cc_start: 0.7405 (mtt180) cc_final: 0.7110 (tpt170) REVERT: R 411 LEU cc_start: 0.8844 (mt) cc_final: 0.8258 (tt) REVERT: R 427 THR cc_start: 0.8537 (m) cc_final: 0.7916 (p) REVERT: R 445 MET cc_start: 0.8092 (mmm) cc_final: 0.7671 (mmp) REVERT: R 474 TRP cc_start: 0.6062 (t60) cc_final: 0.5717 (t60) REVERT: A 19 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8577 (tt0) REVERT: A 31 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8249 (tm-30) REVERT: A 229 ASP cc_start: 0.8285 (m-30) cc_final: 0.8027 (p0) REVERT: A 244 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7700 (mt) REVERT: A 349 SER cc_start: 0.9131 (t) cc_final: 0.8905 (p) REVERT: A 379 CYS cc_start: 0.8290 (t) cc_final: 0.8000 (t) REVERT: A 392 GLU cc_start: 0.7183 (tt0) cc_final: 0.6737 (tp30) REVERT: B 58 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8755 (mp) REVERT: B 138 GLU cc_start: 0.8234 (pp20) cc_final: 0.7990 (pp20) REVERT: B 148 CYS cc_start: 0.9152 (t) cc_final: 0.8596 (t) REVERT: B 163 ASP cc_start: 0.7786 (p0) cc_final: 0.7372 (p0) REVERT: B 169 TRP cc_start: 0.8722 (m100) cc_final: 0.8144 (m100) REVERT: B 175 GLN cc_start: 0.8290 (tt0) cc_final: 0.7996 (tm-30) REVERT: B 235 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8029 (t80) REVERT: B 254 ASP cc_start: 0.7737 (t0) cc_final: 0.7410 (t0) REVERT: B 273 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8109 (mp) REVERT: B 333 ASP cc_start: 0.7660 (t0) cc_final: 0.7383 (t0) REVERT: B 334 SER cc_start: 0.8918 (m) cc_final: 0.8427 (t) REVERT: G 21 MET cc_start: 0.6783 (mmm) cc_final: 0.6422 (mmt) REVERT: G 27 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7206 (mpt180) REVERT: G 58 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8204 (mm-30) REVERT: N 34 MET cc_start: 0.7801 (mtp) cc_final: 0.7493 (mtt) REVERT: N 38 ARG cc_start: 0.7412 (ptt90) cc_final: 0.7164 (ptm-80) REVERT: N 58 ILE cc_start: 0.8477 (mt) cc_final: 0.8254 (mt) REVERT: N 80 TYR cc_start: 0.7655 (m-80) cc_final: 0.7217 (m-80) REVERT: N 98 ARG cc_start: 0.8890 (ttp80) cc_final: 0.8505 (tmm-80) REVERT: N 104 THR cc_start: 0.7785 (t) cc_final: 0.7434 (t) outliers start: 34 outliers final: 25 residues processed: 237 average time/residue: 0.0967 time to fit residues: 32.2181 Evaluate side-chains 236 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 354 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 413 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 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 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 218 CYS Chi-restraints excluded: chain B residue 232 ILE 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 Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 0.0050 chunk 42 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4037 r_free = 0.4037 target = 0.150770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110593 restraints weight = 15839.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.114901 restraints weight = 7186.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117735 restraints weight = 4519.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.119491 restraints weight = 3422.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120484 restraints weight = 2897.545| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9729 Z= 0.124 Angle : 0.648 10.811 13201 Z= 0.330 Chirality : 0.042 0.333 1473 Planarity : 0.004 0.060 1633 Dihedral : 4.954 43.054 1767 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.34 % Allowed : 24.90 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1135 helix: 1.92 (0.25), residues: 439 sheet: 0.56 (0.33), residues: 224 loop : -0.55 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.014 0.001 TYR R 278 PHE 0.031 0.001 PHE R 291 TRP 0.063 0.001 TRP R 298 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9723) covalent geometry : angle 0.64770 (13189) SS BOND : bond 0.00325 ( 6) SS BOND : angle 1.11994 ( 12) hydrogen bonds : bond 0.03333 ( 421) hydrogen bonds : angle 4.17469 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.59 seconds wall clock time: 35 minutes 38.64 seconds (2138.64 seconds total)