Starting phenix.real_space_refine on Sun Jul 27 21:40:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nbh_0411/07_2025/6nbh_0411.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbh_0411/07_2025/6nbh_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_0411/07_2025/6nbh_0411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbh_0411/07_2025/6nbh_0411.map" model { file = "/net/cci-nas-00/data/ceres_data/6nbh_0411/07_2025/6nbh_0411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbh_0411/07_2025/6nbh_0411.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.49, per 1000 atoms: 0.58 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.11 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: 2.61 Time building geometry restraints manager: 3.00 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.370 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (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 TRP 0.015 0.002 TRP R 437 HIS 0.009 0.001 HIS R 114 PHE 0.013 0.002 PHE R 138 TYR 0.016 0.002 TYR N 80 ARG 0.002 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.14799 ( 421) hydrogen bonds : angle 6.99698 ( 1209) SS BOND : bond 0.00540 ( 6) SS BOND : angle 2.09711 ( 12) covalent geometry : bond 0.00526 ( 9723) covalent geometry : angle 0.86491 (13189) *********************** 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 : 0.944 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: 0.7402 (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: 0.7958 (mt) REVERT: B 184 THR cc_start: 0.8151 (p) cc_final: 0.7918 (t) REVERT: B 303 ASP cc_start: 0.9190 (t70) cc_final: 0.8773 (p0) REVERT: N 29 PHE cc_start: 0.8684 (t80) cc_final: 0.8320 (t80) REVERT: N 31 ASN cc_start: 0.8484 (m-40) cc_final: 0.8281 (t0) REVERT: N 57 SER cc_start: 0.9014 (t) cc_final: 0.8760 (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: 0.2511 time to fit residues: 147.8977 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 : 1.118 ------------------------------------------------------------------------------- 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 94 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 140 HIS R 295 ASN R 364 GLN R 402 GLN R 451 GLN P 32 HIS A 271 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.154813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113199 restraints weight = 15789.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.117514 restraints weight = 7456.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.120416 restraints weight = 4781.284| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9729 Z= 0.168 Angle : 0.640 8.891 13201 Z= 0.337 Chirality : 0.044 0.201 1473 Planarity : 0.005 0.059 1633 Dihedral : 5.852 47.990 1768 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.66 % Allowed : 14.27 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1135 helix: 1.24 (0.25), residues: 443 sheet: -0.21 (0.33), residues: 216 loop : -1.06 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 298 HIS 0.007 0.001 HIS A 362 PHE 0.022 0.002 PHE B 235 TYR 0.020 0.002 TYR R 191 ARG 0.009 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 421) hydrogen bonds : angle 4.80188 ( 1209) SS BOND : bond 0.00446 ( 6) SS BOND : angle 1.03415 ( 12) covalent geometry : bond 0.00382 ( 9723) covalent geometry : angle 0.63907 (13189) *********************** 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 312 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 134 TYR cc_start: 0.7725 (p90) cc_final: 0.7511 (p90) REVERT: R 216 HIS cc_start: 0.8172 (m90) cc_final: 0.7388 (m170) REVERT: R 327 PHE cc_start: 0.8713 (t80) cc_final: 0.8486 (t80) REVERT: R 353 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8700 (t0) REVERT: R 404 ARG cc_start: 0.7407 (mtt180) cc_final: 0.7006 (tpt170) REVERT: R 408 LYS cc_start: 0.8068 (tttt) cc_final: 0.7822 (tttm) REVERT: R 438 GLN cc_start: 0.7912 (mt0) cc_final: 0.7684 (mt0) REVERT: R 457 ILE cc_start: 0.9031 (tp) cc_final: 0.8808 (tp) REVERT: R 474 TRP cc_start: 0.5912 (t60) cc_final: 0.5622 (t60) REVERT: P 17 ASP cc_start: 0.8496 (t70) cc_final: 0.8235 (t70) REVERT: A 19 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8704 (mt0) REVERT: A 31 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8010 (tm-30) REVERT: A 229 ASP cc_start: 0.8111 (m-30) cc_final: 0.7411 (p0) REVERT: B 120 ILE cc_start: 0.8700 (mt) cc_final: 0.8340 (mm) REVERT: B 127 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7811 (mttp) REVERT: B 138 GLU cc_start: 0.8097 (pp20) cc_final: 0.7795 (pp20) REVERT: B 169 TRP cc_start: 0.8785 (m100) cc_final: 0.8393 (m100) REVERT: B 175 GLN cc_start: 0.8441 (tt0) cc_final: 0.7976 (tm-30) REVERT: B 235 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8294 (t80) REVERT: B 298 ASP cc_start: 0.8769 (t0) cc_final: 0.8211 (p0) REVERT: B 303 ASP cc_start: 0.8449 (t70) cc_final: 0.7671 (p0) REVERT: N 31 ASN cc_start: 0.8831 (m-40) cc_final: 0.8403 (t0) REVERT: N 38 ARG cc_start: 0.7361 (ptt90) cc_final: 0.7042 (ptm-80) REVERT: N 43 LYS cc_start: 0.6621 (mmtt) cc_final: 0.6421 (mmmt) REVERT: N 80 TYR cc_start: 0.7542 (m-80) cc_final: 0.7322 (m-80) REVERT: N 98 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8484 (ttt-90) REVERT: N 123 GLN cc_start: 0.8330 (tp40) cc_final: 0.7936 (tp-100) outliers start: 46 outliers final: 29 residues processed: 299 average time/residue: 0.2179 time to fit residues: 88.8287 Evaluate side-chains 258 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 189 MET 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 349 THR Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 425 MET Chi-restraints excluded: chain P residue 23 PHE Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL 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 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 30 VAL 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 22 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 239 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.155232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.113613 restraints weight = 15961.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118026 restraints weight = 7444.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.121023 restraints weight = 4729.655| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9729 Z= 0.124 Angle : 0.559 6.626 13201 Z= 0.294 Chirality : 0.041 0.162 1473 Planarity : 0.004 0.045 1633 Dihedral : 5.394 40.968 1767 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.15 % Allowed : 17.41 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1135 helix: 1.66 (0.25), residues: 441 sheet: 0.17 (0.33), residues: 214 loop : -0.92 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 298 HIS 0.004 0.001 HIS R 114 PHE 0.023 0.001 PHE B 235 TYR 0.016 0.001 TYR R 191 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 421) hydrogen bonds : angle 4.37034 ( 1209) SS BOND : bond 0.00445 ( 6) SS BOND : angle 0.86430 ( 12) covalent geometry : bond 0.00281 ( 9723) covalent geometry : angle 0.55823 (13189) *********************** 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 287 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 216 HIS cc_start: 0.8324 (m90) cc_final: 0.8061 (m90) REVERT: R 309 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8384 (tp) REVERT: R 321 LEU cc_start: 0.8525 (tp) cc_final: 0.7835 (tt) REVERT: R 353 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8548 (t0) REVERT: R 404 ARG cc_start: 0.7459 (mtt180) cc_final: 0.7095 (tpt170) REVERT: R 408 LYS cc_start: 0.8151 (tttt) cc_final: 0.7931 (tttm) REVERT: R 457 ILE cc_start: 0.9052 (tp) cc_final: 0.8837 (tp) REVERT: R 474 TRP cc_start: 0.5807 (t60) cc_final: 0.5539 (t60) REVERT: P 16 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8770 (mm-40) REVERT: A 19 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8675 (mt0) REVERT: A 31 GLN cc_start: 0.8879 (mm-40) cc_final: 0.7995 (tm-30) REVERT: A 268 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7999 (tm-30) REVERT: B 58 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8912 (mp) REVERT: B 120 ILE cc_start: 0.8521 (mt) cc_final: 0.8202 (mm) REVERT: B 138 GLU cc_start: 0.8120 (pp20) cc_final: 0.7848 (pp20) REVERT: B 148 CYS cc_start: 0.9309 (t) cc_final: 0.8886 (t) REVERT: B 165 THR cc_start: 0.8183 (p) cc_final: 0.7975 (p) REVERT: B 169 TRP cc_start: 0.8754 (m100) cc_final: 0.8279 (m100) REVERT: B 175 GLN cc_start: 0.8417 (tt0) cc_final: 0.7971 (tm-30) REVERT: B 235 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8240 (t80) REVERT: B 312 ASP cc_start: 0.6766 (p0) cc_final: 0.6436 (p0) REVERT: N 31 ASN cc_start: 0.8886 (m-40) cc_final: 0.8405 (t0) REVERT: N 34 MET cc_start: 0.7899 (mtp) cc_final: 0.7426 (mtm) REVERT: N 38 ARG cc_start: 0.7274 (ptt90) cc_final: 0.6993 (ptm-80) REVERT: N 43 LYS cc_start: 0.6530 (mmtt) cc_final: 0.6307 (mmmt) REVERT: N 58 ILE cc_start: 0.8362 (mt) cc_final: 0.8141 (mt) REVERT: N 80 TYR cc_start: 0.7271 (m-80) cc_final: 0.6940 (m-80) REVERT: N 91 THR cc_start: 0.7272 (OUTLIER) cc_final: 0.7027 (t) REVERT: N 93 VAL cc_start: 0.8008 (t) cc_final: 0.7588 (p) REVERT: N 123 GLN cc_start: 0.8324 (tp40) cc_final: 0.8002 (tp-100) outliers start: 41 outliers final: 20 residues processed: 275 average time/residue: 0.2162 time to fit residues: 81.9071 Evaluate side-chains 242 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 425 MET Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 58 ILE 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 235 PHE 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 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 1 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 97 optimal weight: 0.0870 chunk 72 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 259 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 = 0.4081 r_free = 0.4081 target = 0.156311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.114738 restraints weight = 15946.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119208 restraints weight = 7442.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122224 restraints weight = 4724.194| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 9729 Z= 0.105 Angle : 0.540 6.401 13201 Z= 0.284 Chirality : 0.040 0.158 1473 Planarity : 0.004 0.044 1633 Dihedral : 5.048 37.009 1767 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.05 % Allowed : 19.53 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1135 helix: 1.93 (0.25), residues: 441 sheet: 0.36 (0.32), residues: 219 loop : -0.74 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 298 HIS 0.004 0.001 HIS R 114 PHE 0.023 0.001 PHE B 235 TYR 0.024 0.001 TYR R 134 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 421) hydrogen bonds : angle 4.14319 ( 1209) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.62216 ( 12) covalent geometry : bond 0.00240 ( 9723) covalent geometry : angle 0.53978 (13189) *********************** 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 269 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 216 HIS cc_start: 0.8450 (m90) cc_final: 0.8130 (m90) REVERT: R 231 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7548 (ttp) REVERT: R 309 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8369 (tp) REVERT: R 321 LEU cc_start: 0.8543 (tp) cc_final: 0.7869 (tt) REVERT: R 404 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7129 (tpt170) REVERT: R 411 LEU cc_start: 0.8805 (mt) cc_final: 0.8074 (tt) REVERT: R 441 MET cc_start: 0.8266 (tpp) cc_final: 0.7485 (mmt) REVERT: R 457 ILE cc_start: 0.9036 (tp) cc_final: 0.8815 (tp) REVERT: R 474 TRP cc_start: 0.5821 (t60) cc_final: 0.5525 (t60) REVERT: P 10 GLN cc_start: 0.8995 (mm110) cc_final: 0.8655 (mm110) REVERT: P 20 ARG cc_start: 0.8536 (ttp80) cc_final: 0.7911 (ttp80) REVERT: A 19 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8675 (mt0) REVERT: A 31 GLN cc_start: 0.8894 (mm-40) cc_final: 0.7984 (tm-30) REVERT: A 244 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7802 (mt) REVERT: A 268 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7922 (tp30) REVERT: A 392 GLU cc_start: 0.7209 (tt0) cc_final: 0.6743 (tm-30) REVERT: B 58 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8816 (mp) REVERT: B 120 ILE cc_start: 0.8476 (mt) cc_final: 0.8257 (mm) REVERT: B 138 GLU cc_start: 0.8243 (pp20) cc_final: 0.7936 (pp20) REVERT: B 169 TRP cc_start: 0.8664 (m100) cc_final: 0.8200 (m100) REVERT: B 175 GLN cc_start: 0.8446 (tt0) cc_final: 0.8060 (tm-30) REVERT: B 235 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8174 (t80) REVERT: B 334 SER cc_start: 0.8849 (m) cc_final: 0.8322 (t) REVERT: G 51 LEU cc_start: 0.7449 (mm) cc_final: 0.7057 (mm) REVERT: N 31 ASN cc_start: 0.8943 (m-40) cc_final: 0.8290 (t0) REVERT: N 34 MET cc_start: 0.7912 (mtp) cc_final: 0.7476 (mtt) REVERT: N 38 ARG cc_start: 0.7375 (ptt90) cc_final: 0.6994 (ptm-80) REVERT: N 43 LYS cc_start: 0.6517 (mmtt) cc_final: 0.6219 (mmmt) REVERT: N 58 ILE cc_start: 0.8331 (mt) cc_final: 0.8101 (mt) REVERT: N 80 TYR cc_start: 0.7381 (m-80) cc_final: 0.7037 (m-80) REVERT: N 91 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.6989 (t) REVERT: N 93 VAL cc_start: 0.8050 (t) cc_final: 0.7655 (p) REVERT: N 123 GLN cc_start: 0.8357 (tp40) cc_final: 0.8070 (tp-100) outliers start: 40 outliers final: 25 residues processed: 259 average time/residue: 0.2149 time to fit residues: 77.1800 Evaluate side-chains 247 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 231 MET 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 365 VAL 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 R residue 425 MET Chi-restraints excluded: chain R residue 475 SER 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 359 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 235 PHE 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 37 VAL Chi-restraints excluded: chain N residue 77 ASN 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 70 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 402 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.154630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113209 restraints weight = 16013.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.117622 restraints weight = 7370.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.120625 restraints weight = 4653.448| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5280 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= 0.116 Angle : 0.542 7.256 13201 Z= 0.285 Chirality : 0.040 0.181 1473 Planarity : 0.004 0.050 1633 Dihedral : 4.929 38.136 1767 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.45 % Allowed : 20.55 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1135 helix: 1.99 (0.25), residues: 447 sheet: 0.59 (0.34), residues: 213 loop : -0.72 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 352 HIS 0.003 0.001 HIS R 114 PHE 0.023 0.001 PHE B 235 TYR 0.019 0.001 TYR R 134 ARG 0.011 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 421) hydrogen bonds : angle 4.02679 ( 1209) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.91592 ( 12) covalent geometry : bond 0.00268 ( 9723) covalent geometry : angle 0.54124 (13189) *********************** 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 275 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 216 HIS cc_start: 0.8546 (m90) cc_final: 0.8195 (m90) REVERT: R 231 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7459 (ttm) REVERT: R 309 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8351 (tp) REVERT: R 321 LEU cc_start: 0.8575 (tp) cc_final: 0.8125 (tt) REVERT: R 353 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8377 (t0) REVERT: R 404 ARG cc_start: 0.7573 (mtt180) cc_final: 0.7254 (tpt170) REVERT: R 411 LEU cc_start: 0.8813 (mt) cc_final: 0.8082 (tt) REVERT: R 457 ILE cc_start: 0.9082 (tp) cc_final: 0.8854 (tp) REVERT: R 474 TRP cc_start: 0.5797 (t60) cc_final: 0.5504 (t60) REVERT: P 16 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8804 (mm-40) REVERT: A 19 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8555 (tt0) REVERT: A 31 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8123 (tm-30) REVERT: A 244 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7737 (mt) REVERT: A 268 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8084 (tp30) REVERT: A 392 GLU cc_start: 0.7040 (tt0) cc_final: 0.6629 (tp30) REVERT: B 58 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8815 (mp) REVERT: B 120 ILE cc_start: 0.8532 (mt) cc_final: 0.8251 (mm) REVERT: B 138 GLU cc_start: 0.8257 (pp20) cc_final: 0.7946 (pp20) REVERT: B 169 TRP cc_start: 0.8642 (m100) cc_final: 0.8050 (m100) REVERT: B 175 GLN cc_start: 0.8474 (tt0) cc_final: 0.8104 (tm-30) REVERT: B 235 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8107 (t80) REVERT: B 273 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8404 (mp) REVERT: B 334 SER cc_start: 0.8846 (m) cc_final: 0.8311 (t) REVERT: G 48 ASP cc_start: 0.8112 (p0) cc_final: 0.7746 (p0) REVERT: N 31 ASN cc_start: 0.9068 (m-40) cc_final: 0.8432 (t0) REVERT: N 38 ARG cc_start: 0.7459 (ptt90) cc_final: 0.7047 (ptm-80) REVERT: N 43 LYS cc_start: 0.6527 (mmtt) cc_final: 0.6187 (mmmt) REVERT: N 58 ILE cc_start: 0.8342 (mt) cc_final: 0.8118 (mt) REVERT: N 80 TYR cc_start: 0.7433 (m-80) cc_final: 0.7181 (m-80) REVERT: N 91 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7068 (t) REVERT: N 93 VAL cc_start: 0.8112 (t) cc_final: 0.7733 (p) REVERT: N 104 THR cc_start: 0.8299 (t) cc_final: 0.7934 (t) REVERT: N 123 GLN cc_start: 0.8340 (tp40) cc_final: 0.8079 (tp-100) outliers start: 44 outliers final: 29 residues processed: 264 average time/residue: 0.2197 time to fit residues: 79.8217 Evaluate side-chains 257 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 231 MET 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 365 VAL 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 R residue 425 MET Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 29 THR 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 235 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 280 LYS 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 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.0060 chunk 79 optimal weight: 0.0030 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 402 GLN A 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.154569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113362 restraints weight = 15945.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117712 restraints weight = 7369.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120691 restraints weight = 4661.456| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9729 Z= 0.108 Angle : 0.548 7.059 13201 Z= 0.286 Chirality : 0.040 0.157 1473 Planarity : 0.004 0.067 1633 Dihedral : 4.810 39.605 1767 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.15 % Allowed : 21.46 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1135 helix: 2.05 (0.25), residues: 447 sheet: 0.79 (0.35), residues: 213 loop : -0.64 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 352 HIS 0.003 0.001 HIS R 114 PHE 0.023 0.001 PHE B 235 TYR 0.024 0.001 TYR R 134 ARG 0.011 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 421) hydrogen bonds : angle 3.96950 ( 1209) SS BOND : bond 0.00222 ( 6) SS BOND : angle 0.88870 ( 12) covalent geometry : bond 0.00250 ( 9723) covalent geometry : angle 0.54764 (13189) *********************** 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 269 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 216 HIS cc_start: 0.8509 (m90) cc_final: 0.8101 (m90) REVERT: R 231 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7408 (ttm) REVERT: R 309 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8353 (tp) REVERT: R 321 LEU cc_start: 0.8600 (tp) cc_final: 0.8123 (tt) REVERT: R 353 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8264 (t0) REVERT: R 404 ARG cc_start: 0.7548 (mtt180) cc_final: 0.7236 (tpt170) REVERT: R 411 LEU cc_start: 0.8654 (mt) cc_final: 0.7874 (tt) REVERT: R 413 LEU cc_start: 0.9195 (tp) cc_final: 0.8904 (tt) REVERT: R 474 TRP cc_start: 0.5832 (t60) cc_final: 0.5515 (t60) REVERT: P 16 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8926 (mm-40) REVERT: A 19 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8569 (tt0) REVERT: A 31 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8197 (tm-30) REVERT: A 230 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8364 (mm-30) REVERT: A 244 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7726 (mt) REVERT: A 392 GLU cc_start: 0.7151 (tt0) cc_final: 0.6720 (tp30) REVERT: B 58 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8802 (mp) REVERT: B 111 TYR cc_start: 0.8655 (m-10) cc_final: 0.8302 (m-80) REVERT: B 120 ILE cc_start: 0.8554 (mt) cc_final: 0.8259 (mm) REVERT: B 138 GLU cc_start: 0.8263 (pp20) cc_final: 0.7962 (pp20) REVERT: B 163 ASP cc_start: 0.7459 (p0) cc_final: 0.6865 (p0) REVERT: B 169 TRP cc_start: 0.8611 (m100) cc_final: 0.7977 (m100) REVERT: B 175 GLN cc_start: 0.8443 (tt0) cc_final: 0.8081 (tm-30) REVERT: B 235 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8099 (t80) REVERT: B 270 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8429 (tp) REVERT: B 273 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8329 (mp) REVERT: B 334 SER cc_start: 0.8827 (m) cc_final: 0.8279 (t) REVERT: G 48 ASP cc_start: 0.8118 (p0) cc_final: 0.7852 (p0) REVERT: N 31 ASN cc_start: 0.9086 (m-40) cc_final: 0.8408 (t0) REVERT: N 34 MET cc_start: 0.7528 (mtm) cc_final: 0.7327 (mtp) REVERT: N 58 ILE cc_start: 0.8370 (mt) cc_final: 0.8150 (mt) REVERT: N 91 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7144 (t) REVERT: N 93 VAL cc_start: 0.8134 (t) cc_final: 0.7760 (p) REVERT: N 104 THR cc_start: 0.8160 (t) cc_final: 0.7830 (t) REVERT: N 123 GLN cc_start: 0.8361 (tp40) cc_final: 0.8086 (tp-100) outliers start: 41 outliers final: 25 residues processed: 258 average time/residue: 0.2192 time to fit residues: 78.5004 Evaluate side-chains 240 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 231 MET 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 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 58 ILE 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 235 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 280 LYS 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 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 103 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 402 GLN A 267 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 = 0.4045 r_free = 0.4045 target = 0.153143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.111799 restraints weight = 16014.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.116209 restraints weight = 7343.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119171 restraints weight = 4622.068| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9729 Z= 0.118 Angle : 0.564 8.064 13201 Z= 0.292 Chirality : 0.040 0.157 1473 Planarity : 0.004 0.066 1633 Dihedral : 4.805 38.242 1767 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.06 % Allowed : 21.46 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1135 helix: 2.03 (0.25), residues: 446 sheet: 0.81 (0.35), residues: 215 loop : -0.56 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.003 0.001 HIS R 114 PHE 0.022 0.001 PHE B 235 TYR 0.020 0.001 TYR R 134 ARG 0.013 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 421) hydrogen bonds : angle 3.99137 ( 1209) SS BOND : bond 0.00225 ( 6) SS BOND : angle 0.90591 ( 12) covalent geometry : bond 0.00276 ( 9723) covalent geometry : angle 0.56335 (13189) *********************** 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 266 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 THR cc_start: 0.8460 (p) cc_final: 0.8111 (t) REVERT: R 216 HIS cc_start: 0.8501 (m90) cc_final: 0.8064 (m90) REVERT: R 309 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8318 (tp) REVERT: R 321 LEU cc_start: 0.8623 (tp) cc_final: 0.8408 (tt) REVERT: R 353 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8243 (t0) REVERT: R 404 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7331 (tpt170) REVERT: R 411 LEU cc_start: 0.8603 (mt) cc_final: 0.7812 (tt) REVERT: R 413 LEU cc_start: 0.9218 (tp) cc_final: 0.8933 (tt) REVERT: R 419 VAL cc_start: 0.8678 (m) cc_final: 0.8447 (p) REVERT: R 474 TRP cc_start: 0.5845 (t60) cc_final: 0.5512 (t60) REVERT: P 16 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8858 (mm-40) REVERT: A 31 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8168 (tm-30) REVERT: A 230 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8423 (mm-30) REVERT: A 244 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7704 (mt) REVERT: A 386 MET cc_start: 0.8123 (ttm) cc_final: 0.7875 (tmm) REVERT: A 392 GLU cc_start: 0.7177 (tt0) cc_final: 0.6785 (tp30) REVERT: B 58 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8870 (mp) REVERT: B 111 TYR cc_start: 0.8768 (m-10) cc_final: 0.8456 (m-80) REVERT: B 120 ILE cc_start: 0.8545 (mt) cc_final: 0.8213 (mm) REVERT: B 138 GLU cc_start: 0.8274 (pp20) cc_final: 0.7970 (pp20) REVERT: B 163 ASP cc_start: 0.7465 (p0) cc_final: 0.6895 (p0) REVERT: B 169 TRP cc_start: 0.8635 (m100) cc_final: 0.8011 (m100) REVERT: B 175 GLN cc_start: 0.8440 (tt0) cc_final: 0.8047 (tm-30) REVERT: B 227 SER cc_start: 0.9282 (t) cc_final: 0.8452 (p) REVERT: B 235 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8081 (t80) REVERT: B 245 SER cc_start: 0.8492 (t) cc_final: 0.7565 (t) REVERT: B 270 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8394 (tp) REVERT: B 273 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8308 (mp) REVERT: B 334 SER cc_start: 0.8849 (m) cc_final: 0.8324 (t) REVERT: N 31 ASN cc_start: 0.9129 (m-40) cc_final: 0.8408 (t0) REVERT: N 58 ILE cc_start: 0.8431 (mt) cc_final: 0.8229 (mt) REVERT: N 65 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8530 (tppt) REVERT: N 91 THR cc_start: 0.7415 (OUTLIER) cc_final: 0.7158 (t) REVERT: N 104 THR cc_start: 0.8074 (t) cc_final: 0.7730 (t) REVERT: N 123 GLN cc_start: 0.8328 (tp40) cc_final: 0.8113 (tp-100) outliers start: 50 outliers final: 29 residues processed: 255 average time/residue: 0.2300 time to fit residues: 80.8920 Evaluate side-chains 249 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 365 VAL 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 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 29 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 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 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 74 ASN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.144533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103097 restraints weight = 16317.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107121 restraints weight = 7720.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109757 restraints weight = 4973.157| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9729 Z= 0.249 Angle : 0.735 7.552 13201 Z= 0.382 Chirality : 0.046 0.185 1473 Planarity : 0.004 0.056 1633 Dihedral : 5.921 37.926 1767 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.26 % Allowed : 22.27 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1135 helix: 1.62 (0.24), residues: 447 sheet: 0.25 (0.34), residues: 238 loop : -0.44 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 47 HIS 0.011 0.002 HIS A 220 PHE 0.024 0.002 PHE B 235 TYR 0.028 0.002 TYR R 191 ARG 0.012 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 421) hydrogen bonds : angle 4.43196 ( 1209) SS BOND : bond 0.00555 ( 6) SS BOND : angle 1.39216 ( 12) covalent geometry : bond 0.00568 ( 9723) covalent geometry : angle 0.73375 (13189) *********************** 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 263 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 THR cc_start: 0.8929 (p) cc_final: 0.8717 (t) REVERT: R 309 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8238 (tp) REVERT: R 353 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8312 (t0) REVERT: R 372 VAL cc_start: 0.8518 (m) cc_final: 0.8256 (p) REVERT: R 474 TRP cc_start: 0.6007 (t60) cc_final: 0.5690 (t60) REVERT: P 16 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8830 (mm-40) REVERT: A 31 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8155 (tm-30) REVERT: A 229 ASP cc_start: 0.8204 (m-30) cc_final: 0.7949 (p0) REVERT: A 268 GLU cc_start: 0.8181 (tp30) cc_final: 0.7975 (tp30) REVERT: A 349 SER cc_start: 0.9319 (t) cc_final: 0.9045 (p) REVERT: A 392 GLU cc_start: 0.7320 (tt0) cc_final: 0.6744 (tm-30) REVERT: B 138 GLU cc_start: 0.8245 (pp20) cc_final: 0.7877 (pp20) REVERT: B 163 ASP cc_start: 0.7852 (p0) cc_final: 0.7496 (p0) REVERT: B 175 GLN cc_start: 0.8405 (tt0) cc_final: 0.7907 (tm-30) REVERT: B 235 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8177 (t80) REVERT: B 245 SER cc_start: 0.8698 (t) cc_final: 0.8357 (t) REVERT: B 273 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8195 (mp) REVERT: B 333 ASP cc_start: 0.7736 (t0) cc_final: 0.7420 (t0) REVERT: B 334 SER cc_start: 0.8925 (m) cc_final: 0.8537 (t) REVERT: G 21 MET cc_start: 0.7006 (mmm) cc_final: 0.6670 (mmt) REVERT: N 32 TYR cc_start: 0.8777 (m-10) cc_final: 0.8339 (m-10) REVERT: N 47 TRP cc_start: 0.7261 (t60) cc_final: 0.6812 (t60) REVERT: N 65 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8740 (tppt) REVERT: N 91 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7568 (t) REVERT: N 93 VAL cc_start: 0.8279 (t) cc_final: 0.8022 (p) REVERT: N 123 GLN cc_start: 0.8457 (tp40) cc_final: 0.8108 (tp-100) outliers start: 52 outliers final: 33 residues processed: 251 average time/residue: 0.2191 time to fit residues: 75.7379 Evaluate side-chains 233 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 183 VAL 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 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 353 ASP Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 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 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 29 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 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 G residue 30 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 R 448 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.105329 restraints weight = 16168.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.109461 restraints weight = 7508.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.112154 restraints weight = 4783.576| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9729 Z= 0.184 Angle : 0.693 10.656 13201 Z= 0.354 Chirality : 0.044 0.160 1473 Planarity : 0.004 0.056 1633 Dihedral : 5.525 40.730 1767 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.45 % Allowed : 23.38 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1135 helix: 1.60 (0.24), residues: 450 sheet: 0.35 (0.34), residues: 235 loop : -0.47 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 47 HIS 0.008 0.001 HIS A 220 PHE 0.023 0.002 PHE B 235 TYR 0.020 0.001 TYR R 191 ARG 0.014 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 421) hydrogen bonds : angle 4.37541 ( 1209) SS BOND : bond 0.00401 ( 6) SS BOND : angle 1.49659 ( 12) covalent geometry : bond 0.00428 ( 9723) covalent geometry : angle 0.69196 (13189) *********************** 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 262 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.6172 (mtp) cc_final: 0.5835 (ptp) REVERT: R 192 THR cc_start: 0.8838 (p) cc_final: 0.8578 (t) REVERT: R 309 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8282 (tp) REVERT: R 353 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8317 (t0) REVERT: R 411 LEU cc_start: 0.9175 (mm) cc_final: 0.8350 (tt) REVERT: R 474 TRP cc_start: 0.5967 (t60) cc_final: 0.5645 (t60) REVERT: A 31 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8181 (tm-30) REVERT: A 229 ASP cc_start: 0.8213 (m-30) cc_final: 0.7982 (p0) REVERT: A 244 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7844 (mt) REVERT: A 349 SER cc_start: 0.9263 (t) cc_final: 0.9000 (p) REVERT: A 392 GLU cc_start: 0.7211 (tt0) cc_final: 0.6719 (tp30) REVERT: B 138 GLU cc_start: 0.8203 (pp20) cc_final: 0.7868 (pp20) REVERT: B 163 ASP cc_start: 0.7850 (p0) cc_final: 0.7485 (p0) REVERT: B 169 TRP cc_start: 0.8830 (m100) cc_final: 0.8416 (m100) REVERT: B 175 GLN cc_start: 0.8359 (tt0) cc_final: 0.7973 (tm-30) REVERT: B 235 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8165 (t80) REVERT: B 245 SER cc_start: 0.8649 (t) cc_final: 0.8218 (t) REVERT: B 273 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8215 (mp) REVERT: B 333 ASP cc_start: 0.7801 (t0) cc_final: 0.7534 (t0) REVERT: B 334 SER cc_start: 0.8935 (m) cc_final: 0.8555 (t) REVERT: G 21 MET cc_start: 0.7065 (mmm) cc_final: 0.6580 (mmt) REVERT: G 27 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7247 (mpt180) REVERT: N 32 TYR cc_start: 0.8665 (m-10) cc_final: 0.8253 (m-10) REVERT: N 47 TRP cc_start: 0.7348 (t60) cc_final: 0.6936 (t60) REVERT: N 65 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8731 (tppt) REVERT: N 83 MET cc_start: 0.5668 (mmm) cc_final: 0.5205 (mmm) REVERT: N 90 ASP cc_start: 0.8001 (m-30) cc_final: 0.7617 (m-30) REVERT: N 91 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7616 (t) REVERT: N 93 VAL cc_start: 0.8432 (t) cc_final: 0.8192 (p) REVERT: N 103 PHE cc_start: 0.8775 (m-80) cc_final: 0.8564 (m-80) REVERT: N 104 THR cc_start: 0.7984 (t) cc_final: 0.7624 (t) REVERT: N 123 GLN cc_start: 0.8569 (tp40) cc_final: 0.8065 (tp-100) outliers start: 44 outliers final: 35 residues processed: 246 average time/residue: 0.2371 time to fit residues: 81.7004 Evaluate side-chains 247 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 198 SER 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 353 ASP Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 440 GLN Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE 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 378 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.149071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.108364 restraints weight = 16020.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112680 restraints weight = 7323.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.115509 restraints weight = 4610.518| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9729 Z= 0.135 Angle : 0.679 10.091 13201 Z= 0.342 Chirality : 0.042 0.157 1473 Planarity : 0.004 0.055 1633 Dihedral : 5.223 42.011 1767 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.35 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1135 helix: 1.74 (0.25), residues: 446 sheet: 0.45 (0.33), residues: 232 loop : -0.52 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP N 47 HIS 0.006 0.001 HIS A 220 PHE 0.026 0.001 PHE R 424 TYR 0.017 0.001 TYR R 191 ARG 0.014 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 421) hydrogen bonds : angle 4.23111 ( 1209) SS BOND : bond 0.00285 ( 6) SS BOND : angle 1.11507 ( 12) covalent geometry : bond 0.00316 ( 9723) covalent geometry : angle 0.67803 (13189) ********************** 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 256 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 THR cc_start: 0.8758 (p) cc_final: 0.8420 (t) REVERT: R 309 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8361 (tp) REVERT: R 353 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8343 (t0) REVERT: R 411 LEU cc_start: 0.8934 (mm) cc_final: 0.8209 (tt) REVERT: R 474 TRP cc_start: 0.5906 (t60) cc_final: 0.5616 (t60) REVERT: A 31 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8199 (tm-30) REVERT: A 58 LYS cc_start: 0.7571 (tmtt) cc_final: 0.7157 (mtpp) REVERT: A 229 ASP cc_start: 0.8263 (m-30) cc_final: 0.7954 (p0) REVERT: A 244 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7821 (mt) REVERT: A 349 SER cc_start: 0.9158 (t) cc_final: 0.8922 (p) REVERT: A 386 MET cc_start: 0.8151 (ttm) cc_final: 0.7945 (tmm) REVERT: A 392 GLU cc_start: 0.7229 (tt0) cc_final: 0.6783 (tp30) REVERT: B 138 GLU cc_start: 0.8256 (pp20) cc_final: 0.7963 (pp20) REVERT: B 163 ASP cc_start: 0.7729 (p0) cc_final: 0.7289 (p0) REVERT: B 169 TRP cc_start: 0.8776 (m100) cc_final: 0.8303 (m100) REVERT: B 175 GLN cc_start: 0.8355 (tt0) cc_final: 0.8005 (tm-30) REVERT: B 235 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8063 (t80) REVERT: B 254 ASP cc_start: 0.7799 (t0) cc_final: 0.7496 (t0) REVERT: B 260 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: B 273 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8223 (mp) REVERT: B 297 TRP cc_start: 0.9254 (m100) cc_final: 0.9011 (m100) REVERT: B 333 ASP cc_start: 0.7699 (t0) cc_final: 0.7444 (t0) REVERT: B 334 SER cc_start: 0.8895 (m) cc_final: 0.8514 (t) REVERT: G 21 MET cc_start: 0.6830 (mmm) cc_final: 0.6528 (mmt) REVERT: G 27 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7215 (mpt180) REVERT: N 32 TYR cc_start: 0.8496 (m-10) cc_final: 0.8160 (m-10) REVERT: N 47 TRP cc_start: 0.7148 (t60) cc_final: 0.6695 (t60) REVERT: N 65 LYS cc_start: 0.9144 (ttpt) cc_final: 0.8731 (tppt) REVERT: N 83 MET cc_start: 0.5427 (mmm) cc_final: 0.5206 (mmm) REVERT: N 91 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7544 (t) REVERT: N 93 VAL cc_start: 0.8433 (t) cc_final: 0.8185 (p) REVERT: N 103 PHE cc_start: 0.8635 (m-80) cc_final: 0.8101 (m-80) REVERT: N 104 THR cc_start: 0.7765 (t) cc_final: 0.7441 (t) REVERT: N 123 GLN cc_start: 0.8592 (tp40) cc_final: 0.8149 (tp-100) outliers start: 33 outliers final: 26 residues processed: 245 average time/residue: 0.2394 time to fit residues: 81.3655 Evaluate side-chains 243 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 440 GLN Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE 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 29 THR 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 234 PHE 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 12 VAL Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 0.0670 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 HIS R 295 ASN R 402 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109033 restraints weight = 16037.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.113255 restraints weight = 7293.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.116121 restraints weight = 4577.990| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.7006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9729 Z= 0.139 Angle : 0.681 10.997 13201 Z= 0.341 Chirality : 0.042 0.220 1473 Planarity : 0.004 0.055 1633 Dihedral : 5.172 42.704 1767 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.34 % Allowed : 25.20 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1135 helix: 1.74 (0.25), residues: 444 sheet: 0.49 (0.34), residues: 230 loop : -0.44 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 47 HIS 0.007 0.001 HIS A 220 PHE 0.023 0.001 PHE B 235 TYR 0.018 0.001 TYR R 443 ARG 0.014 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 421) hydrogen bonds : angle 4.22419 ( 1209) SS BOND : bond 0.00294 ( 6) SS BOND : angle 0.98205 ( 12) covalent geometry : bond 0.00326 ( 9723) covalent geometry : angle 0.68069 (13189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4018.12 seconds wall clock time: 71 minutes 3.72 seconds (4263.72 seconds total)