Starting phenix.real_space_refine on Fri Feb 14 03:53:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nbh_0411/02_2025/6nbh_0411.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbh_0411/02_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_0411/02_2025/6nbh_0411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbh_0411/02_2025/6nbh_0411.map" model { file = "/net/cci-nas-00/data/ceres_data/6nbh_0411/02_2025/6nbh_0411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbh_0411/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.74, per 1000 atoms: 0.60 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: 2.36 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: 0.97 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: 2.45 Time building geometry restraints manager: 2.73 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.760 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- 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 9723 Z= 0.340 Angle : 0.865 6.871 13189 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 *********************** 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 : 1.077 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: 0.2566 time to fit residues: 149.9693 Evaluate side-chains 247 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 = 51)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113192 restraints weight = 15789.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.117524 restraints weight = 7459.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120368 restraints weight = 4777.783| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 9723 Z= 0.246 Angle : 0.639 8.891 13189 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 *********************** 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 : 1.009 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: 0.7510 (p90) REVERT: R 216 HIS cc_start: 0.8167 (m90) cc_final: 0.7385 (m170) REVERT: R 327 PHE cc_start: 0.8713 (t80) cc_final: 0.8487 (t80) REVERT: R 353 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8701 (t0) REVERT: R 404 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7008 (tpt170) REVERT: R 408 LYS cc_start: 0.8074 (tttt) cc_final: 0.7828 (tttm) REVERT: R 438 GLN cc_start: 0.7912 (mt0) cc_final: 0.7683 (mt0) REVERT: R 457 ILE cc_start: 0.9034 (tp) cc_final: 0.8810 (tp) REVERT: R 474 TRP cc_start: 0.5913 (t60) cc_final: 0.5623 (t60) REVERT: P 17 ASP cc_start: 0.8496 (t70) cc_final: 0.8234 (t70) REVERT: A 19 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8705 (mt0) REVERT: A 31 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8009 (tm-30) REVERT: A 229 ASP cc_start: 0.8107 (m-30) cc_final: 0.7413 (p0) REVERT: B 120 ILE cc_start: 0.8705 (mt) cc_final: 0.8347 (mm) REVERT: B 127 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7813 (mttp) REVERT: B 138 GLU cc_start: 0.8097 (pp20) cc_final: 0.7796 (pp20) REVERT: B 169 TRP cc_start: 0.8786 (m100) cc_final: 0.8395 (m100) REVERT: B 175 GLN cc_start: 0.8440 (tt0) cc_final: 0.7977 (tm-30) REVERT: B 235 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8297 (t80) REVERT: B 298 ASP cc_start: 0.8768 (t0) cc_final: 0.8211 (p0) REVERT: B 303 ASP cc_start: 0.8448 (t70) cc_final: 0.7673 (p0) REVERT: N 31 ASN cc_start: 0.8831 (m-40) cc_final: 0.8403 (t0) REVERT: N 38 ARG cc_start: 0.7367 (ptt90) cc_final: 0.7048 (ptm-80) REVERT: N 43 LYS cc_start: 0.6623 (mmtt) cc_final: 0.6423 (mmmt) REVERT: N 80 TYR cc_start: 0.7541 (m-80) cc_final: 0.7320 (m-80) REVERT: N 98 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8487 (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: 0.2336 time to fit residues: 94.8566 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 : 1.011 ------------------------------------------------------------------------------- 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: 0.0020 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.156658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.115154 restraints weight = 15930.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.119605 restraints weight = 7395.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.122593 restraints weight = 4692.863| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 9723 Z= 0.162 Angle : 0.551 6.806 13189 Z= 0.289 Chirality : 0.041 0.161 1473 Planarity : 0.004 0.044 1633 Dihedral : 5.349 40.713 1767 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.54 % Allowed : 18.12 % Favored : 78.34 % 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: 0.47 (0.25), residues: 1135 helix: 1.67 (0.25), residues: 441 sheet: 0.20 (0.33), residues: 212 loop : -0.89 (0.27), residues: 482 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 0.014 0.001 TYR R 191 ARG 0.009 0.000 ARG B 214 *********************** 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 286 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 1.069 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: 0.8304 (m90) cc_final: 0.8033 (m90) REVERT: R 309 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8376 (tp) REVERT: R 353 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8548 (t0) REVERT: R 404 ARG cc_start: 0.7429 (mtt180) cc_final: 0.7067 (tpt170) REVERT: R 408 LYS cc_start: 0.8137 (tttt) cc_final: 0.7920 (tttm) REVERT: R 457 ILE cc_start: 0.9013 (tp) cc_final: 0.8796 (tp) REVERT: R 474 TRP cc_start: 0.5795 (t60) cc_final: 0.5511 (t60) REVERT: A 19 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8668 (mt0) REVERT: A 31 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8015 (tm-30) REVERT: A 221 MET cc_start: 0.8301 (ttm) cc_final: 0.7962 (ttm) REVERT: A 268 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 120 ILE cc_start: 0.8526 (mt) cc_final: 0.8219 (mm) REVERT: B 138 GLU cc_start: 0.8147 (pp20) cc_final: 0.7870 (pp20) REVERT: B 148 CYS cc_start: 0.9311 (t) cc_final: 0.8873 (t) REVERT: B 169 TRP cc_start: 0.8727 (m100) cc_final: 0.8140 (m100) REVERT: B 175 GLN cc_start: 0.8401 (tt0) cc_final: 0.7941 (tm-30) REVERT: B 235 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8220 (t80) REVERT: B 312 ASP cc_start: 0.6785 (p0) cc_final: 0.6559 (p0) REVERT: N 31 ASN cc_start: 0.8843 (m-40) cc_final: 0.8399 (t0) REVERT: N 34 MET cc_start: 0.7881 (mtp) cc_final: 0.7414 (mtm) REVERT: N 38 ARG cc_start: 0.7265 (ptt90) cc_final: 0.6998 (ptm-80) REVERT: N 43 LYS cc_start: 0.6514 (mmtt) cc_final: 0.6299 (mmmt) REVERT: N 80 TYR cc_start: 0.7264 (m-80) cc_final: 0.6927 (m-80) REVERT: N 91 THR cc_start: 0.7216 (OUTLIER) cc_final: 0.6956 (t) REVERT: N 93 VAL cc_start: 0.7985 (t) cc_final: 0.7571 (p) REVERT: N 98 ARG cc_start: 0.8855 (ttp80) cc_final: 0.8598 (ttt-90) REVERT: N 123 GLN cc_start: 0.8300 (tp40) cc_final: 0.7996 (tp-100) outliers start: 35 outliers final: 17 residues processed: 277 average time/residue: 0.2212 time to fit residues: 84.7692 Evaluate side-chains 236 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 385 LEU 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 235 PHE Chi-restraints excluded: chain B residue 307 VAL 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: 6.9990 chunk 96 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.155751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113977 restraints weight = 16029.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118463 restraints weight = 7419.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121441 restraints weight = 4691.002| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9723 Z= 0.165 Angle : 0.544 6.534 13189 Z= 0.285 Chirality : 0.040 0.159 1473 Planarity : 0.004 0.044 1633 Dihedral : 5.073 37.415 1767 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 0.80 (0.25), residues: 1135 helix: 1.94 (0.25), residues: 441 sheet: 0.45 (0.33), residues: 218 loop : -0.76 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 298 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.001 PHE B 235 TYR 0.025 0.001 TYR R 134 ARG 0.010 0.000 ARG B 214 *********************** 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 274 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 216 HIS cc_start: 0.8432 (m90) cc_final: 0.8146 (m90) REVERT: R 231 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7654 (ttp) REVERT: R 309 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8368 (tp) REVERT: R 321 LEU cc_start: 0.8565 (tp) cc_final: 0.8103 (tt) REVERT: R 404 ARG cc_start: 0.7501 (mtt180) cc_final: 0.7184 (tpt170) REVERT: R 411 LEU cc_start: 0.8852 (mt) cc_final: 0.8099 (tt) REVERT: R 457 ILE cc_start: 0.9027 (tp) cc_final: 0.8807 (tp) REVERT: R 474 TRP cc_start: 0.5695 (t60) cc_final: 0.5433 (t60) REVERT: P 10 GLN cc_start: 0.9005 (mm110) cc_final: 0.8664 (mm110) REVERT: P 17 ASP cc_start: 0.8530 (t70) cc_final: 0.8258 (t70) REVERT: P 20 ARG cc_start: 0.8553 (ttp80) cc_final: 0.7930 (ttp80) REVERT: A 19 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8672 (mt0) REVERT: A 31 GLN cc_start: 0.8896 (mm-40) cc_final: 0.7980 (tm-30) REVERT: A 244 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7780 (mt) REVERT: A 268 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7948 (tp30) REVERT: A 392 GLU cc_start: 0.7206 (tt0) cc_final: 0.6620 (tm-30) REVERT: B 120 ILE cc_start: 0.8451 (mt) cc_final: 0.8235 (mm) REVERT: B 138 GLU cc_start: 0.8247 (pp20) cc_final: 0.7940 (pp20) REVERT: B 169 TRP cc_start: 0.8656 (m100) cc_final: 0.8194 (m100) REVERT: B 175 GLN cc_start: 0.8459 (tt0) cc_final: 0.8071 (tm-30) REVERT: B 235 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8166 (t80) REVERT: B 262 MET cc_start: 0.7205 (ttm) cc_final: 0.6944 (ttt) REVERT: B 334 SER cc_start: 0.8797 (m) cc_final: 0.8255 (t) REVERT: G 51 LEU cc_start: 0.7352 (mm) cc_final: 0.7010 (mm) REVERT: N 31 ASN cc_start: 0.9006 (m-40) cc_final: 0.8411 (t0) REVERT: N 34 MET cc_start: 0.7913 (mtp) cc_final: 0.7472 (mtt) REVERT: N 38 ARG cc_start: 0.7333 (ptt90) cc_final: 0.6945 (ptm-80) REVERT: N 43 LYS cc_start: 0.6497 (mmtt) cc_final: 0.6189 (mmmt) REVERT: N 80 TYR cc_start: 0.7413 (m-80) cc_final: 0.7070 (m-80) REVERT: N 91 THR cc_start: 0.7230 (OUTLIER) cc_final: 0.6982 (t) REVERT: N 93 VAL cc_start: 0.8030 (t) cc_final: 0.7620 (p) REVERT: N 123 GLN cc_start: 0.8343 (tp40) cc_final: 0.8055 (tp-100) outliers start: 40 outliers final: 26 residues processed: 263 average time/residue: 0.2234 time to fit residues: 80.5633 Evaluate side-chains 255 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 365 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 410 THR Chi-restraints excluded: chain 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 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 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 235 PHE 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: 0.9990 chunk 83 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 89 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.155291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114019 restraints weight = 16042.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.118410 restraints weight = 7368.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.121405 restraints weight = 4643.242| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9723 Z= 0.165 Angle : 0.544 7.435 13189 Z= 0.285 Chirality : 0.040 0.158 1473 Planarity : 0.004 0.049 1633 Dihedral : 4.942 38.531 1767 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.55 % Allowed : 20.04 % Favored : 75.40 % 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: 0.94 (0.25), residues: 1135 helix: 2.04 (0.25), residues: 441 sheet: 0.66 (0.34), residues: 213 loop : -0.74 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP R 352 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.001 PHE B 235 TYR 0.019 0.001 TYR R 134 ARG 0.010 0.000 ARG B 214 *********************** 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 270 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 134 TYR cc_start: 0.7032 (p90) cc_final: 0.6794 (p90) REVERT: R 216 HIS cc_start: 0.8445 (m90) cc_final: 0.8096 (m90) REVERT: R 231 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7756 (ttp) REVERT: R 309 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8364 (tp) REVERT: R 321 LEU cc_start: 0.8594 (tp) cc_final: 0.8101 (tt) REVERT: R 353 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8249 (t0) REVERT: R 404 ARG cc_start: 0.7594 (mtt180) cc_final: 0.7262 (tpt170) REVERT: R 441 MET cc_start: 0.8461 (tpp) cc_final: 0.8135 (mmm) REVERT: R 457 ILE cc_start: 0.9019 (tp) cc_final: 0.8808 (tp) REVERT: R 474 TRP cc_start: 0.5739 (t60) cc_final: 0.5439 (t60) REVERT: P 16 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8753 (mm-40) REVERT: A 19 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8556 (tt0) REVERT: A 31 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8093 (tm-30) REVERT: A 51 SER cc_start: 0.7025 (m) cc_final: 0.6824 (p) REVERT: A 244 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7778 (mt) REVERT: A 268 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8055 (tp30) REVERT: A 392 GLU cc_start: 0.7078 (tt0) cc_final: 0.6594 (tm-30) REVERT: B 46 ARG cc_start: 0.7276 (mtp85) cc_final: 0.7056 (mmm-85) REVERT: B 120 ILE cc_start: 0.8529 (mt) cc_final: 0.8246 (mm) REVERT: B 138 GLU cc_start: 0.8256 (pp20) cc_final: 0.7945 (pp20) REVERT: B 169 TRP cc_start: 0.8669 (m100) cc_final: 0.8055 (m100) REVERT: B 175 GLN cc_start: 0.8468 (tt0) cc_final: 0.8109 (tm-30) REVERT: B 235 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8099 (t80) REVERT: B 273 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 334 SER cc_start: 0.8696 (m) cc_final: 0.8262 (t) REVERT: G 48 ASP cc_start: 0.8012 (p0) cc_final: 0.7624 (p0) REVERT: N 31 ASN cc_start: 0.9049 (m-40) cc_final: 0.8431 (t0) REVERT: N 38 ARG cc_start: 0.7447 (ptt90) cc_final: 0.7009 (ptm-80) REVERT: N 43 LYS cc_start: 0.6546 (mmtt) cc_final: 0.6193 (mmmt) REVERT: N 80 TYR cc_start: 0.7447 (m-80) cc_final: 0.7116 (m-80) REVERT: N 91 THR cc_start: 0.7278 (OUTLIER) cc_final: 0.7030 (t) REVERT: N 93 VAL cc_start: 0.8093 (t) cc_final: 0.7710 (p) REVERT: N 104 THR cc_start: 0.8333 (t) cc_final: 0.7969 (t) REVERT: N 123 GLN cc_start: 0.8339 (tp40) cc_final: 0.8061 (tp-100) outliers start: 45 outliers final: 30 residues processed: 257 average time/residue: 0.2172 time to fit residues: 77.6338 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 : 1.013 ------------------------------------------------------------------------------- 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 349 THR Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 29 THR 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 161 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP 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 77 ASN 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: 0.0010 chunk 79 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.153580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112230 restraints weight = 16033.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.116555 restraints weight = 7400.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119556 restraints weight = 4680.159| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9723 Z= 0.183 Angle : 0.557 8.239 13189 Z= 0.291 Chirality : 0.041 0.165 1473 Planarity : 0.004 0.067 1633 Dihedral : 4.925 34.997 1767 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.05 % Allowed : 20.95 % 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: 0.97 (0.25), residues: 1135 helix: 2.00 (0.25), residues: 447 sheet: 0.69 (0.35), residues: 213 loop : -0.70 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 352 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.001 PHE B 235 TYR 0.016 0.001 TYR R 134 ARG 0.011 0.000 ARG B 214 *********************** 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 263 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 216 HIS cc_start: 0.8558 (m90) cc_final: 0.8236 (m90) REVERT: R 231 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7446 (ttm) REVERT: R 309 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8336 (tp) REVERT: R 321 LEU cc_start: 0.8624 (tp) cc_final: 0.8405 (tt) REVERT: R 353 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8146 (t0) REVERT: R 404 ARG cc_start: 0.7548 (mtt180) cc_final: 0.7278 (tpt170) REVERT: R 411 LEU cc_start: 0.8802 (mt) cc_final: 0.7987 (tt) REVERT: R 457 ILE cc_start: 0.9120 (tp) cc_final: 0.8909 (tp) REVERT: R 474 TRP cc_start: 0.5787 (t60) cc_final: 0.5450 (t60) REVERT: A 19 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8566 (tt0) REVERT: A 31 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8168 (tm-30) REVERT: A 230 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8289 (mm-30) REVERT: A 244 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7717 (mt) REVERT: A 392 GLU cc_start: 0.7173 (tt0) cc_final: 0.6688 (tp30) REVERT: B 111 TYR cc_start: 0.8826 (m-10) cc_final: 0.8528 (m-80) REVERT: B 120 ILE cc_start: 0.8535 (mt) cc_final: 0.8245 (mm) REVERT: B 138 GLU cc_start: 0.8234 (pp20) cc_final: 0.7928 (pp20) REVERT: B 169 TRP cc_start: 0.8662 (m100) cc_final: 0.8072 (m100) REVERT: B 175 GLN cc_start: 0.8462 (tt0) cc_final: 0.8086 (tm-30) REVERT: B 235 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8116 (t80) REVERT: B 245 SER cc_start: 0.8414 (t) cc_final: 0.8054 (t) REVERT: B 273 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8359 (mp) REVERT: B 334 SER cc_start: 0.8568 (m) cc_final: 0.8118 (t) REVERT: N 31 ASN cc_start: 0.9079 (m-40) cc_final: 0.8417 (t0) REVERT: N 34 MET cc_start: 0.7554 (mtm) cc_final: 0.7296 (mtp) REVERT: N 38 ARG cc_start: 0.7475 (ptt90) cc_final: 0.7074 (ptm-80) REVERT: N 43 LYS cc_start: 0.6615 (mmtt) cc_final: 0.6265 (mmmt) REVERT: N 80 TYR cc_start: 0.7456 (m-80) cc_final: 0.7112 (m-80) REVERT: N 91 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.7144 (t) REVERT: N 93 VAL cc_start: 0.8119 (t) cc_final: 0.7744 (p) REVERT: N 104 THR cc_start: 0.8195 (t) cc_final: 0.7881 (t) REVERT: N 123 GLN cc_start: 0.8361 (tp40) cc_final: 0.8079 (tp-100) outliers start: 40 outliers final: 27 residues processed: 253 average time/residue: 0.2244 time to fit residues: 78.0270 Evaluate side-chains 247 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 228 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 A 267 GLN ** 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 = 0.4020 r_free = 0.4020 target = 0.150936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.109123 restraints weight = 16120.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113340 restraints weight = 7577.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116194 restraints weight = 4862.773| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9723 Z= 0.213 Angle : 0.582 7.546 13189 Z= 0.305 Chirality : 0.042 0.159 1473 Planarity : 0.004 0.086 1633 Dihedral : 5.054 32.386 1767 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.86 % Allowed : 21.66 % 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: 0.99 (0.25), residues: 1135 helix: 1.93 (0.25), residues: 447 sheet: 0.68 (0.34), residues: 218 loop : -0.58 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 47 HIS 0.003 0.001 HIS A 220 PHE 0.023 0.001 PHE B 235 TYR 0.024 0.001 TYR R 134 ARG 0.012 0.000 ARG B 214 *********************** 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 268 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 THR cc_start: 0.8644 (p) cc_final: 0.8340 (t) REVERT: R 216 HIS cc_start: 0.8577 (m90) cc_final: 0.8217 (m90) REVERT: R 309 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8312 (tp) REVERT: R 404 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7310 (tpt170) REVERT: R 411 LEU cc_start: 0.8565 (mt) cc_final: 0.7791 (tt) REVERT: R 413 LEU cc_start: 0.9202 (tp) cc_final: 0.8961 (tt) REVERT: R 419 VAL cc_start: 0.8773 (m) cc_final: 0.8483 (p) REVERT: A 19 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8558 (tt0) REVERT: A 31 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8199 (tm-30) REVERT: A 229 ASP cc_start: 0.8120 (m-30) cc_final: 0.7599 (p0) REVERT: A 244 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7770 (mt) REVERT: A 392 GLU cc_start: 0.7132 (tt0) cc_final: 0.6788 (tp30) REVERT: B 46 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7607 (mmm-85) REVERT: B 111 TYR cc_start: 0.8970 (m-10) cc_final: 0.8679 (m-80) REVERT: B 120 ILE cc_start: 0.8600 (mt) cc_final: 0.8258 (mm) REVERT: B 138 GLU cc_start: 0.8216 (pp20) cc_final: 0.7886 (pp20) REVERT: B 169 TRP cc_start: 0.8697 (m100) cc_final: 0.8214 (m100) REVERT: B 175 GLN cc_start: 0.8475 (tt0) cc_final: 0.8064 (tm-30) REVERT: B 235 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8072 (t80) REVERT: B 245 SER cc_start: 0.8579 (t) cc_final: 0.8131 (t) REVERT: B 273 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 333 ASP cc_start: 0.7567 (t0) cc_final: 0.7333 (t0) REVERT: B 334 SER cc_start: 0.8662 (m) cc_final: 0.8285 (t) REVERT: N 31 ASN cc_start: 0.9180 (m-40) cc_final: 0.8443 (t0) REVERT: N 34 MET cc_start: 0.7636 (mtm) cc_final: 0.7326 (mtp) REVERT: N 38 ARG cc_start: 0.7482 (ptt90) cc_final: 0.7109 (ptm-80) REVERT: N 65 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8594 (tppt) REVERT: N 68 PHE cc_start: 0.8204 (m-10) cc_final: 0.7858 (m-10) REVERT: N 91 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7261 (t) REVERT: N 93 VAL cc_start: 0.8145 (t) cc_final: 0.7872 (p) REVERT: N 104 THR cc_start: 0.8121 (t) cc_final: 0.7775 (t) REVERT: N 123 GLN cc_start: 0.8367 (tp40) cc_final: 0.7833 (tp-100) outliers start: 48 outliers final: 34 residues processed: 258 average time/residue: 0.2247 time to fit residues: 80.9218 Evaluate side-chains 247 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 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 368 LEU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 410 THR Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 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 74 SER 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 228 ASP 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=2.00 ------------------------------------------------------------------------------- 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: 4.9990 chunk 5 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.143580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101951 restraints weight = 16536.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106031 restraints weight = 7755.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108662 restraints weight = 4978.305| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 9723 Z= 0.391 Angle : 0.729 7.684 13189 Z= 0.381 Chirality : 0.047 0.188 1473 Planarity : 0.005 0.068 1633 Dihedral : 6.015 40.307 1767 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.67 % Allowed : 21.36 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.25), residues: 1135 helix: 1.48 (0.24), residues: 446 sheet: 0.35 (0.34), residues: 236 loop : -0.52 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP N 47 HIS 0.009 0.002 HIS A 220 PHE 0.024 0.002 PHE B 235 TYR 0.028 0.002 TYR R 191 ARG 0.014 0.001 ARG B 22 *********************** 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 268 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.6417 (mtm) cc_final: 0.5981 (ptp) REVERT: R 309 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8226 (tp) REVERT: R 404 ARG cc_start: 0.7499 (mtt180) cc_final: 0.7295 (tpt170) REVERT: P 20 ARG cc_start: 0.8868 (ttp80) cc_final: 0.8343 (ptt-90) REVERT: A 19 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8591 (tt0) REVERT: A 31 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8174 (tm-30) REVERT: A 229 ASP cc_start: 0.8260 (m-30) cc_final: 0.8059 (p0) REVERT: A 349 SER cc_start: 0.9305 (t) cc_final: 0.9027 (p) REVERT: A 392 GLU cc_start: 0.7377 (tt0) cc_final: 0.6721 (tm-30) REVERT: B 138 GLU cc_start: 0.8222 (pp20) cc_final: 0.7881 (pp20) REVERT: B 163 ASP cc_start: 0.7903 (p0) cc_final: 0.7573 (p0) REVERT: B 175 GLN cc_start: 0.8393 (tt0) cc_final: 0.7872 (tm-30) REVERT: B 235 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8033 (t80) REVERT: B 273 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8377 (mp) REVERT: B 333 ASP cc_start: 0.7802 (t0) cc_final: 0.7565 (t0) REVERT: B 334 SER cc_start: 0.8815 (m) cc_final: 0.8537 (t) REVERT: G 48 ASP cc_start: 0.8256 (p0) cc_final: 0.7725 (p0) REVERT: N 31 ASN cc_start: 0.9395 (m110) cc_final: 0.9172 (m110) REVERT: N 32 TYR cc_start: 0.8726 (m-10) cc_final: 0.8263 (m-10) REVERT: N 34 MET cc_start: 0.7722 (mtm) cc_final: 0.7356 (mtp) REVERT: N 38 ARG cc_start: 0.7539 (ptt90) cc_final: 0.6741 (ptm-80) REVERT: N 47 TRP cc_start: 0.7467 (t60) cc_final: 0.6989 (t60) REVERT: N 65 LYS cc_start: 0.9130 (ttpt) cc_final: 0.8739 (tppt) REVERT: N 91 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7629 (t) REVERT: N 93 VAL cc_start: 0.8324 (t) cc_final: 0.7993 (p) REVERT: N 123 GLN cc_start: 0.8405 (tp40) cc_final: 0.8044 (tp-100) outliers start: 56 outliers final: 36 residues processed: 256 average time/residue: 0.2255 time to fit residues: 78.8371 Evaluate side-chains 237 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 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 410 THR Chi-restraints excluded: chain P residue 15 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 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 289 LEU 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 235 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN R 402 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107323 restraints weight = 16048.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111579 restraints weight = 7272.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.114407 restraints weight = 4564.664| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9723 Z= 0.215 Angle : 0.664 10.823 13189 Z= 0.340 Chirality : 0.043 0.203 1473 Planarity : 0.004 0.073 1633 Dihedral : 5.396 42.814 1767 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.34 % Allowed : 24.70 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.25), residues: 1135 helix: 1.68 (0.24), residues: 448 sheet: 0.40 (0.33), residues: 233 loop : -0.51 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 47 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.001 PHE B 235 TYR 0.021 0.001 TYR R 134 ARG 0.014 0.001 ARG B 214 *********************** 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 258 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.6229 (mtm) cc_final: 0.5801 (ptp) REVERT: R 216 HIS cc_start: 0.8345 (m90) cc_final: 0.7944 (m90) REVERT: R 309 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8269 (tp) REVERT: R 380 ASN cc_start: 0.9022 (t0) cc_final: 0.8514 (t0) REVERT: R 404 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7236 (tpt170) REVERT: R 411 LEU cc_start: 0.9125 (mm) cc_final: 0.8338 (tt) REVERT: R 413 LEU cc_start: 0.9172 (tp) cc_final: 0.8943 (tt) REVERT: A 19 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8581 (tt0) REVERT: A 31 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8208 (tm-30) REVERT: A 229 ASP cc_start: 0.8256 (m-30) cc_final: 0.7999 (p0) REVERT: A 244 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7757 (mt) REVERT: A 349 SER cc_start: 0.9154 (t) cc_final: 0.8914 (p) REVERT: A 386 MET cc_start: 0.8249 (ttm) cc_final: 0.7996 (tmm) REVERT: A 392 GLU cc_start: 0.7126 (tt0) cc_final: 0.6658 (tp30) REVERT: B 138 GLU cc_start: 0.8206 (pp20) cc_final: 0.7867 (pp20) REVERT: B 163 ASP cc_start: 0.7805 (p0) cc_final: 0.7452 (p0) REVERT: B 169 TRP cc_start: 0.8800 (m100) cc_final: 0.8380 (m100) REVERT: B 175 GLN cc_start: 0.8384 (tt0) cc_final: 0.8008 (tm-30) REVERT: B 235 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7998 (t80) REVERT: B 254 ASP cc_start: 0.7876 (t0) cc_final: 0.7580 (t0) REVERT: B 260 GLU cc_start: 0.8507 (pm20) cc_final: 0.8264 (pm20) REVERT: B 273 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8291 (mp) REVERT: B 297 TRP cc_start: 0.9279 (m100) cc_final: 0.8970 (m100) REVERT: B 325 MET cc_start: 0.8733 (mmm) cc_final: 0.8030 (mtm) REVERT: B 333 ASP cc_start: 0.7667 (t0) cc_final: 0.7388 (t0) REVERT: B 334 SER cc_start: 0.8718 (m) cc_final: 0.8362 (t) REVERT: G 21 MET cc_start: 0.6919 (mmm) cc_final: 0.6386 (mmt) REVERT: G 27 ARG cc_start: 0.7808 (mtt90) cc_final: 0.7316 (mpt-90) REVERT: G 48 ASP cc_start: 0.8038 (p0) cc_final: 0.7587 (p0) REVERT: N 32 TYR cc_start: 0.8580 (m-10) cc_final: 0.8346 (m-10) REVERT: N 38 ARG cc_start: 0.7330 (ptt90) cc_final: 0.6999 (ptm-80) REVERT: N 65 LYS cc_start: 0.9149 (ttpt) cc_final: 0.8720 (tppt) REVERT: N 82 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7779 (tm-30) REVERT: N 91 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7651 (t) REVERT: N 93 VAL cc_start: 0.8326 (t) cc_final: 0.8050 (p) REVERT: N 104 THR cc_start: 0.7859 (t) cc_final: 0.7563 (t) REVERT: N 123 GLN cc_start: 0.8547 (tp40) cc_final: 0.8121 (tp-100) outliers start: 33 outliers final: 27 residues processed: 250 average time/residue: 0.2136 time to fit residues: 74.1723 Evaluate side-chains 244 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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 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 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 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 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 10.9990 chunk 22 optimal weight: 0.0870 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 HIS R 402 GLN R 448 ASN N 74 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 = 0.4001 r_free = 0.4001 target = 0.149136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.108850 restraints weight = 16043.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113166 restraints weight = 7210.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.116073 restraints weight = 4510.769| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9723 Z= 0.199 Angle : 0.660 9.996 13189 Z= 0.338 Chirality : 0.042 0.162 1473 Planarity : 0.004 0.067 1633 Dihedral : 5.233 43.915 1767 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.14 % Allowed : 24.39 % 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: 0.82 (0.25), residues: 1135 helix: 1.73 (0.25), residues: 444 sheet: 0.45 (0.33), residues: 232 loop : -0.53 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 47 HIS 0.004 0.001 HIS A 220 PHE 0.024 0.001 PHE N 68 TYR 0.022 0.001 TYR R 134 ARG 0.014 0.000 ARG B 214 ********************** 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 257 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8269 (tp) REVERT: R 380 ASN cc_start: 0.9019 (t0) cc_final: 0.8389 (t0) REVERT: R 402 GLN cc_start: 0.8367 (mm110) cc_final: 0.7984 (mm-40) REVERT: R 404 ARG cc_start: 0.7495 (mtt180) cc_final: 0.7222 (tpt170) REVERT: R 411 LEU cc_start: 0.9007 (mm) cc_final: 0.8237 (tt) REVERT: R 413 LEU cc_start: 0.9091 (tp) cc_final: 0.8839 (tt) REVERT: P 20 ARG cc_start: 0.8981 (tmm-80) cc_final: 0.8484 (ptt-90) REVERT: A 19 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8579 (tt0) REVERT: A 31 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8255 (tm-30) REVERT: A 58 LYS cc_start: 0.7564 (tmtt) cc_final: 0.7158 (mmmt) REVERT: A 229 ASP cc_start: 0.8301 (m-30) cc_final: 0.7981 (p0) REVERT: A 244 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7697 (mt) REVERT: A 349 SER cc_start: 0.9153 (t) cc_final: 0.8913 (p) REVERT: A 386 MET cc_start: 0.8145 (ttm) cc_final: 0.7921 (tmm) REVERT: A 392 GLU cc_start: 0.7217 (tt0) cc_final: 0.6793 (tp30) REVERT: B 138 GLU cc_start: 0.8205 (pp20) cc_final: 0.7878 (pp20) REVERT: B 163 ASP cc_start: 0.7662 (p0) cc_final: 0.7263 (p0) REVERT: B 169 TRP cc_start: 0.8780 (m100) cc_final: 0.8306 (m100) REVERT: B 175 GLN cc_start: 0.8366 (tt0) cc_final: 0.8015 (tm-30) REVERT: B 217 MET cc_start: 0.7494 (ptp) cc_final: 0.7187 (ptm) REVERT: B 235 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8022 (t80) REVERT: B 254 ASP cc_start: 0.7801 (t0) cc_final: 0.7492 (t0) REVERT: B 260 GLU cc_start: 0.8502 (pm20) cc_final: 0.8273 (pm20) REVERT: B 273 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8274 (mp) REVERT: B 297 TRP cc_start: 0.9235 (m100) cc_final: 0.9021 (m100) REVERT: B 333 ASP cc_start: 0.7610 (t0) cc_final: 0.7406 (t0) REVERT: B 334 SER cc_start: 0.8696 (m) cc_final: 0.8338 (t) REVERT: G 21 MET cc_start: 0.6787 (mmm) cc_final: 0.6434 (mmt) REVERT: G 27 ARG cc_start: 0.7775 (mtt90) cc_final: 0.7132 (mpt180) REVERT: G 48 ASP cc_start: 0.8063 (p0) cc_final: 0.7670 (p0) REVERT: G 58 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8048 (mm-30) REVERT: N 32 TYR cc_start: 0.8544 (m-10) cc_final: 0.8311 (m-10) REVERT: N 38 ARG cc_start: 0.7357 (ptt90) cc_final: 0.7151 (ptm-80) REVERT: N 53 GLN cc_start: 0.7999 (mp10) cc_final: 0.7303 (mt0) REVERT: N 65 LYS cc_start: 0.9142 (ttpt) cc_final: 0.8753 (tppt) REVERT: N 91 THR cc_start: 0.7898 (OUTLIER) cc_final: 0.7687 (t) REVERT: N 93 VAL cc_start: 0.8268 (t) cc_final: 0.7947 (p) REVERT: N 104 THR cc_start: 0.7663 (t) cc_final: 0.7242 (t) REVERT: N 123 GLN cc_start: 0.8603 (tp40) cc_final: 0.8096 (tp-100) outliers start: 31 outliers final: 26 residues processed: 250 average time/residue: 0.2132 time to fit residues: 73.7958 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 : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 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 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 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 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 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.150154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109580 restraints weight = 15971.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113925 restraints weight = 7274.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.116801 restraints weight = 4573.991| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9723 Z= 0.199 Angle : 0.653 10.559 13189 Z= 0.334 Chirality : 0.042 0.308 1473 Planarity : 0.004 0.067 1633 Dihedral : 5.156 44.650 1767 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.24 % Allowed : 24.60 % 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: 0.83 (0.25), residues: 1135 helix: 1.82 (0.25), residues: 442 sheet: 0.42 (0.33), residues: 232 loop : -0.59 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP N 47 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.001 PHE B 235 TYR 0.022 0.001 TYR R 134 ARG 0.014 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3682.43 seconds wall clock time: 66 minutes 29.33 seconds (3989.33 seconds total)