Starting phenix.real_space_refine on Fri Aug 22 22:39:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zw0_60514/08_2025/8zw0_60514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zw0_60514/08_2025/8zw0_60514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zw0_60514/08_2025/8zw0_60514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zw0_60514/08_2025/8zw0_60514.map" model { file = "/net/cci-nas-00/data/ceres_data/8zw0_60514/08_2025/8zw0_60514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zw0_60514/08_2025/8zw0_60514.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.071 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 58 5.16 5 C 5358 2.51 5 N 1462 2.21 5 O 1553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8431 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1956 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "D" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2385 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 2 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: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'CLR': 2, 'PG2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.03, per 1000 atoms: 0.24 Number of scatterers: 8431 At special positions: 0 Unit cell: (86.87, 97.09, 135.05, 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 58 16.00 O 1553 8.00 N 1462 7.00 C 5358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 485.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.8% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.575A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.661A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.527A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.937A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.597A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'D' and resid 20 through 47 removed outlier: 3.698A pdb=" N GLY D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 26 " --> pdb=" O MET D 22 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 90 removed outlier: 3.524A pdb=" N LEU D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Proline residue: D 81 - end of helix Processing helix chain 'D' and resid 92 through 97 removed outlier: 4.017A pdb=" N ALA D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 136 removed outlier: 3.602A pdb=" N ALA D 109 " --> pdb=" O CYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 144 Processing helix chain 'D' and resid 145 through 165 removed outlier: 3.985A pdb=" N ALA D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Proline residue: D 154 - end of helix Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.734A pdb=" N GLY D 170 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 234 removed outlier: 3.848A pdb=" N TYR D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 234 " --> pdb=" O ARG D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 291 removed outlier: 3.836A pdb=" N HIS D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Proline residue: D 280 - end of helix Processing helix chain 'D' and resid 297 through 313 removed outlier: 3.607A pdb=" N LEU D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.966A pdb=" N ILE D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 328 through 333 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.676A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.601A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.803A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.599A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.853A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.104A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.500A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.705A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.675A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.372A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.774A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 174 through 176 Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.741A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.006A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1371 1.31 - 1.43: 2277 1.43 - 1.56: 4869 1.56 - 1.68: 4 1.68 - 1.81: 83 Bond restraints: 8604 Sorted by residual: bond pdb=" C10 PG2 D 403 " pdb=" C9 PG2 D 403 " ideal model delta sigma weight residual 1.524 1.345 0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C11 PG2 D 403 " pdb=" C12 PG2 D 403 " ideal model delta sigma weight residual 1.524 1.361 0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" CA ALA D 97 " pdb=" C ALA D 97 " ideal model delta sigma weight residual 1.526 1.462 0.063 1.15e-02 7.56e+03 3.02e+01 bond pdb=" C LEU D 78 " pdb=" O LEU D 78 " ideal model delta sigma weight residual 1.236 1.302 -0.066 1.21e-02 6.83e+03 2.94e+01 bond pdb=" C7 PG2 D 403 " pdb=" C8 PG2 D 403 " ideal model delta sigma weight residual 1.526 1.421 0.105 2.00e-02 2.50e+03 2.77e+01 ... (remaining 8599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 11588 4.41 - 8.83: 51 8.83 - 13.24: 4 13.24 - 17.66: 3 17.66 - 22.07: 1 Bond angle restraints: 11647 Sorted by residual: angle pdb=" N ASN D 102 " pdb=" CA ASN D 102 " pdb=" C ASN D 102 " ideal model delta sigma weight residual 113.20 91.13 22.07 1.21e+00 6.83e-01 3.33e+02 angle pdb=" C SER D 195 " pdb=" N VAL D 196 " pdb=" CA VAL D 196 " ideal model delta sigma weight residual 120.42 110.01 10.41 1.42e+00 4.96e-01 5.38e+01 angle pdb=" N ASP D 101 " pdb=" CA ASP D 101 " pdb=" C ASP D 101 " ideal model delta sigma weight residual 108.18 121.57 -13.39 2.01e+00 2.48e-01 4.44e+01 angle pdb=" N LEU D 79 " pdb=" CA LEU D 79 " pdb=" C LEU D 79 " ideal model delta sigma weight residual 111.07 117.55 -6.48 1.07e+00 8.73e-01 3.67e+01 angle pdb=" C4 PG2 D 403 " pdb=" C5 PG2 D 403 " pdb=" C6 PG2 D 403 " ideal model delta sigma weight residual 127.01 111.07 15.94 3.00e+00 1.11e-01 2.82e+01 ... (remaining 11642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.58: 5027 22.58 - 45.15: 164 45.15 - 67.73: 39 67.73 - 90.31: 13 90.31 - 112.88: 3 Dihedral angle restraints: 5246 sinusoidal: 2166 harmonic: 3080 Sorted by residual: dihedral pdb=" C2 CLR D 401 " pdb=" C3 CLR D 401 " pdb=" C4 CLR D 401 " pdb=" C5 CLR D 401 " ideal model delta sinusoidal sigma weight residual -55.03 57.85 -112.88 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" C5 CLR D 401 " pdb=" C3 CLR D 401 " pdb=" C4 CLR D 401 " pdb=" O1 CLR D 401 " ideal model delta sinusoidal sigma weight residual 175.64 65.83 109.81 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C17 PG2 D 403 " pdb=" C15 PG2 D 403 " pdb=" C16 PG2 D 403 " pdb=" O5 PG2 D 403 " ideal model delta sinusoidal sigma weight residual 57.42 -49.82 107.24 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 5243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1178 0.066 - 0.132: 119 0.132 - 0.198: 8 0.198 - 0.263: 5 0.263 - 0.329: 3 Chirality restraints: 1313 Sorted by residual: chirality pdb=" CA LEU D 79 " pdb=" N LEU D 79 " pdb=" C LEU D 79 " pdb=" CB LEU D 79 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C15 PG2 D 403 " pdb=" C14 PG2 D 403 " pdb=" C16 PG2 D 403 " pdb=" O5 PG2 D 403 " both_signs ideal model delta sigma weight residual False 2.23 2.56 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C8 PG2 D 403 " pdb=" C12 PG2 D 403 " pdb=" C7 PG2 D 403 " pdb=" C9 PG2 D 403 " both_signs ideal model delta sigma weight residual False -2.57 -2.86 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1310 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 9 " -0.036 2.00e-02 2.50e+03 7.06e-02 4.98e+01 pdb=" C GLN D 9 " 0.122 2.00e-02 2.50e+03 pdb=" O GLN D 9 " -0.046 2.00e-02 2.50e+03 pdb=" N ASN D 10 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 80 " 0.098 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO D 81 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO D 81 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO D 81 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 74 " 0.022 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C LEU D 74 " -0.075 2.00e-02 2.50e+03 pdb=" O LEU D 74 " 0.027 2.00e-02 2.50e+03 pdb=" N GLY D 75 " 0.026 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 145 2.63 - 3.19: 7866 3.19 - 3.76: 13188 3.76 - 4.33: 18675 4.33 - 4.90: 31231 Nonbonded interactions: 71105 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.057 3.040 nonbonded pdb=" N ASN D 102 " pdb=" N SER D 103 " model vdw 2.116 2.560 nonbonded pdb=" O CYS B 218 " pdb=" NE2 GLN G 18 " model vdw 2.171 3.120 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.189 3.040 nonbonded pdb=" NH1 ARG D 284 " pdb=" OE1 GLU D 304 " model vdw 2.211 3.120 ... (remaining 71100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 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 0.179 8604 Z= 0.338 Angle : 0.732 22.073 11647 Z= 0.418 Chirality : 0.044 0.329 1313 Planarity : 0.005 0.145 1480 Dihedral : 13.060 112.884 3256 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 1.05 % Allowed : 2.49 % Favored : 96.46 % Rotamer: Outliers : 1.55 % Allowed : 4.31 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.26), residues: 1046 helix: 1.13 (0.26), residues: 400 sheet: -1.09 (0.33), residues: 216 loop : -1.47 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 8 TYR 0.005 0.001 TYR D 87 PHE 0.005 0.000 PHE D 290 TRP 0.004 0.000 TRP A 234 HIS 0.005 0.000 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 8604) covalent geometry : angle 0.73228 (11647) hydrogen bonds : bond 0.17710 ( 406) hydrogen bonds : angle 6.60118 ( 1146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: B 243 THR cc_start: 0.8501 (p) cc_final: 0.8266 (p) REVERT: D 43 ARG cc_start: 0.6722 (mtp180) cc_final: 0.5981 (mtt180) REVERT: D 76 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.4356 (mptm) REVERT: D 173 LYS cc_start: 0.6103 (mtpt) cc_final: 0.5771 (tttt) REVERT: D 183 CYS cc_start: 0.8266 (m) cc_final: 0.8029 (m) REVERT: D 276 MET cc_start: 0.6196 (mmt) cc_final: 0.5918 (ptp) REVERT: N 91 THR cc_start: 0.8736 (t) cc_final: 0.8523 (p) REVERT: N 117 TYR cc_start: 0.8063 (m-80) cc_final: 0.7847 (m-80) outliers start: 14 outliers final: 6 residues processed: 235 average time/residue: 0.5561 time to fit residues: 139.2151 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 81 PRO Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 311 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.0170 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 220 GLN B 259 GLN D 102 ASN G 11 GLN G 18 GLN N 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132684 restraints weight = 10392.264| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.40 r_work: 0.3464 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8604 Z= 0.124 Angle : 0.563 7.796 11647 Z= 0.289 Chirality : 0.043 0.184 1313 Planarity : 0.004 0.031 1480 Dihedral : 8.321 100.049 1338 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 3.87 % Allowed : 13.50 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1046 helix: 2.13 (0.26), residues: 396 sheet: -0.41 (0.35), residues: 203 loop : -0.68 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 137 TYR 0.016 0.001 TYR D 87 PHE 0.011 0.001 PHE A 212 TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8604) covalent geometry : angle 0.56333 (11647) hydrogen bonds : bond 0.03495 ( 406) hydrogen bonds : angle 4.45985 ( 1146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.7488 (pm20) cc_final: 0.7151 (pm20) REVERT: A 392 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7784 (mt-10) REVERT: B 46 ARG cc_start: 0.8018 (mtp-110) cc_final: 0.7690 (mtp180) REVERT: B 78 LYS cc_start: 0.7944 (tppp) cc_final: 0.7711 (tppt) REVERT: B 172 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: B 209 LYS cc_start: 0.7785 (mttm) cc_final: 0.7470 (mttp) REVERT: B 214 ARG cc_start: 0.7418 (mpt180) cc_final: 0.7208 (mtt90) REVERT: B 215 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: B 243 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8556 (p) REVERT: B 254 ASP cc_start: 0.7935 (p0) cc_final: 0.7570 (p0) REVERT: D 9 GLN cc_start: 0.6282 (tt0) cc_final: 0.5582 (tp40) REVERT: D 11 THR cc_start: 0.7693 (m) cc_final: 0.7387 (p) REVERT: D 22 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.6200 (tpp) REVERT: D 43 ARG cc_start: 0.6112 (mtp180) cc_final: 0.5087 (mtt180) REVERT: D 74 LEU cc_start: 0.7412 (mt) cc_final: 0.7141 (mm) REVERT: D 76 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.5157 (mptm) REVERT: D 169 MET cc_start: 0.7029 (mtt) cc_final: 0.6816 (ptp) REVERT: D 173 LYS cc_start: 0.6199 (mtpt) cc_final: 0.5749 (tttt) REVERT: D 276 MET cc_start: 0.6732 (mmt) cc_final: 0.5915 (ptp) REVERT: N 89 GLU cc_start: 0.7348 (pp20) cc_final: 0.7016 (pm20) REVERT: N 91 THR cc_start: 0.8265 (t) cc_final: 0.7940 (m) REVERT: N 93 VAL cc_start: 0.8296 (m) cc_final: 0.8086 (p) outliers start: 35 outliers final: 10 residues processed: 158 average time/residue: 0.4855 time to fit residues: 82.4684 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 311 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 95 optimal weight: 0.0670 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 230 ASN B 237 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.161757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122828 restraints weight = 10321.183| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.69 r_work: 0.3341 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8604 Z= 0.124 Angle : 0.525 8.129 11647 Z= 0.270 Chirality : 0.041 0.192 1313 Planarity : 0.004 0.037 1480 Dihedral : 7.727 93.432 1331 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.04 % Rotamer: Outliers : 3.54 % Allowed : 15.27 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.26), residues: 1046 helix: 2.62 (0.26), residues: 389 sheet: -0.09 (0.35), residues: 200 loop : -0.50 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.011 0.001 TYR N 60 PHE 0.019 0.001 PHE D 5 TRP 0.013 0.001 TRP A 234 HIS 0.006 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8604) covalent geometry : angle 0.52511 (11647) hydrogen bonds : bond 0.03444 ( 406) hydrogen bonds : angle 4.19736 ( 1146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6470 (mt-10) REVERT: A 28 LYS cc_start: 0.6868 (ttmt) cc_final: 0.6509 (mttt) REVERT: A 57 VAL cc_start: 0.6933 (t) cc_final: 0.6594 (m) REVERT: A 224 VAL cc_start: 0.8793 (p) cc_final: 0.8463 (t) REVERT: A 311 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: A 314 GLU cc_start: 0.7457 (pm20) cc_final: 0.7199 (pm20) REVERT: B 59 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: B 209 LYS cc_start: 0.7434 (mttm) cc_final: 0.7208 (mttp) REVERT: B 214 ARG cc_start: 0.7413 (mpt180) cc_final: 0.7053 (mtt90) REVERT: B 243 THR cc_start: 0.8377 (p) cc_final: 0.8064 (p) REVERT: B 254 ASP cc_start: 0.7983 (p0) cc_final: 0.7402 (t70) REVERT: D 11 THR cc_start: 0.7458 (m) cc_final: 0.7182 (p) REVERT: D 22 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5842 (tpp) REVERT: D 43 ARG cc_start: 0.5964 (mtp180) cc_final: 0.4949 (mtt180) REVERT: D 91 ARG cc_start: 0.5635 (mtm-85) cc_final: 0.5272 (mtp-110) REVERT: D 95 VAL cc_start: 0.6763 (m) cc_final: 0.6375 (p) REVERT: D 173 LYS cc_start: 0.6329 (mtpt) cc_final: 0.5864 (tttt) REVERT: D 276 MET cc_start: 0.6454 (mmt) cc_final: 0.5646 (ptp) REVERT: D 307 ARG cc_start: 0.6584 (ttm-80) cc_final: 0.5979 (ttm110) REVERT: N 19 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6745 (tmt90) REVERT: N 89 GLU cc_start: 0.7388 (pp20) cc_final: 0.7074 (pp20) REVERT: N 91 THR cc_start: 0.8093 (t) cc_final: 0.7731 (m) REVERT: N 93 VAL cc_start: 0.7999 (m) cc_final: 0.7734 (p) outliers start: 32 outliers final: 12 residues processed: 159 average time/residue: 0.5281 time to fit residues: 89.7259 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 311 PHE Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 64 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 88 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 237 ASN B 239 ASN B 259 GLN D 9 GLN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120506 restraints weight = 10464.642| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.71 r_work: 0.3313 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8604 Z= 0.117 Angle : 0.505 7.034 11647 Z= 0.261 Chirality : 0.041 0.172 1313 Planarity : 0.004 0.042 1480 Dihedral : 7.535 93.469 1327 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.32 % Rotamer: Outliers : 4.09 % Allowed : 16.04 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.26), residues: 1046 helix: 2.75 (0.25), residues: 390 sheet: 0.05 (0.35), residues: 198 loop : -0.37 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 46 TYR 0.010 0.001 TYR D 87 PHE 0.012 0.001 PHE D 5 TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8604) covalent geometry : angle 0.50532 (11647) hydrogen bonds : bond 0.03312 ( 406) hydrogen bonds : angle 4.04610 ( 1146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6604 (mt-10) REVERT: A 28 LYS cc_start: 0.6963 (ttmt) cc_final: 0.6621 (mttt) REVERT: A 224 VAL cc_start: 0.8844 (p) cc_final: 0.8541 (t) REVERT: A 314 GLU cc_start: 0.7424 (pm20) cc_final: 0.7108 (pm20) REVERT: B 46 ARG cc_start: 0.7800 (mtp-110) cc_final: 0.6341 (mpt180) REVERT: B 134 ARG cc_start: 0.6659 (ptm-80) cc_final: 0.6447 (ptt90) REVERT: B 172 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: B 209 LYS cc_start: 0.7436 (mttm) cc_final: 0.7214 (mttp) REVERT: B 214 ARG cc_start: 0.7484 (mpt180) cc_final: 0.6950 (mpt180) REVERT: B 243 THR cc_start: 0.8455 (p) cc_final: 0.8124 (p) REVERT: B 254 ASP cc_start: 0.8052 (p0) cc_final: 0.7578 (t0) REVERT: D 11 THR cc_start: 0.7448 (m) cc_final: 0.7078 (p) REVERT: D 22 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.5851 (tpp) REVERT: D 43 ARG cc_start: 0.5858 (mtp180) cc_final: 0.4861 (mtt180) REVERT: D 91 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.5364 (mtm-85) REVERT: D 173 LYS cc_start: 0.6425 (mtpt) cc_final: 0.5910 (tttt) REVERT: D 276 MET cc_start: 0.6513 (mmt) cc_final: 0.5686 (ptp) REVERT: D 307 ARG cc_start: 0.6550 (ttm-80) cc_final: 0.5958 (ttm110) REVERT: N 19 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6619 (tmt90) REVERT: N 65 LYS cc_start: 0.7671 (ttpt) cc_final: 0.6854 (tptm) REVERT: N 89 GLU cc_start: 0.7467 (pp20) cc_final: 0.7071 (pm20) REVERT: N 91 THR cc_start: 0.8035 (t) cc_final: 0.7708 (m) REVERT: N 93 VAL cc_start: 0.7973 (m) cc_final: 0.7760 (p) outliers start: 37 outliers final: 16 residues processed: 152 average time/residue: 0.5399 time to fit residues: 87.5035 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN D 106 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 = 0.3853 r_free = 0.3853 target = 0.155305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115810 restraints weight = 10413.297| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.62 r_work: 0.3337 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8604 Z= 0.179 Angle : 0.573 10.159 11647 Z= 0.296 Chirality : 0.043 0.166 1313 Planarity : 0.004 0.055 1480 Dihedral : 7.682 100.674 1325 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 4.20 % Allowed : 16.59 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.26), residues: 1046 helix: 2.65 (0.25), residues: 390 sheet: -0.13 (0.34), residues: 204 loop : -0.29 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 46 TYR 0.015 0.002 TYR B 105 PHE 0.014 0.002 PHE B 151 TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8604) covalent geometry : angle 0.57331 (11647) hydrogen bonds : bond 0.03903 ( 406) hydrogen bonds : angle 4.19495 ( 1146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7698 (mm-30) cc_final: 0.6961 (mt-10) REVERT: A 28 LYS cc_start: 0.7200 (ttmt) cc_final: 0.6876 (mttt) REVERT: A 224 VAL cc_start: 0.8895 (p) cc_final: 0.8579 (t) REVERT: A 311 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6613 (m-80) REVERT: A 314 GLU cc_start: 0.7509 (pm20) cc_final: 0.7220 (pm20) REVERT: B 42 ARG cc_start: 0.7142 (ttp-110) cc_final: 0.6675 (ttm110) REVERT: B 46 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.6816 (mpt180) REVERT: B 134 ARG cc_start: 0.6777 (ptm-80) cc_final: 0.6552 (ptt90) REVERT: B 172 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: B 209 LYS cc_start: 0.8033 (mttm) cc_final: 0.7808 (mttp) REVERT: B 214 ARG cc_start: 0.7778 (mpt180) cc_final: 0.7475 (mpt90) REVERT: B 243 THR cc_start: 0.8702 (p) cc_final: 0.8386 (p) REVERT: B 254 ASP cc_start: 0.8295 (p0) cc_final: 0.8018 (t0) REVERT: B 325 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8155 (mmt) REVERT: D 11 THR cc_start: 0.7425 (m) cc_final: 0.6922 (p) REVERT: D 22 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5841 (tpp) REVERT: D 43 ARG cc_start: 0.5796 (mtp180) cc_final: 0.4799 (mtt180) REVERT: D 91 ARG cc_start: 0.5738 (OUTLIER) cc_final: 0.5311 (mtm110) REVERT: D 173 LYS cc_start: 0.6825 (mtpt) cc_final: 0.6272 (ttpt) REVERT: D 276 MET cc_start: 0.6632 (mmt) cc_final: 0.5725 (ptp) REVERT: D 307 ARG cc_start: 0.6940 (ttm-80) cc_final: 0.6275 (ttp80) REVERT: N 19 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6799 (tmt90) REVERT: N 76 LYS cc_start: 0.7853 (ptpt) cc_final: 0.7618 (ptpp) REVERT: N 89 GLU cc_start: 0.7655 (pp20) cc_final: 0.7248 (pm20) REVERT: N 91 THR cc_start: 0.8220 (t) cc_final: 0.7857 (m) outliers start: 38 outliers final: 18 residues processed: 152 average time/residue: 0.6146 time to fit residues: 99.3729 Evaluate side-chains 144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117699 restraints weight = 10339.714| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.58 r_work: 0.3306 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8604 Z= 0.115 Angle : 0.495 6.284 11647 Z= 0.258 Chirality : 0.040 0.150 1313 Planarity : 0.004 0.035 1480 Dihedral : 7.440 94.130 1325 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.04 % Rotamer: Outliers : 3.43 % Allowed : 18.58 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.26), residues: 1046 helix: 2.86 (0.25), residues: 391 sheet: -0.07 (0.34), residues: 198 loop : -0.25 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 105 TYR 0.010 0.001 TYR A 339 PHE 0.013 0.001 PHE B 199 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8604) covalent geometry : angle 0.49521 (11647) hydrogen bonds : bond 0.03326 ( 406) hydrogen bonds : angle 4.01814 ( 1146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6720 (mt-10) REVERT: A 28 LYS cc_start: 0.7080 (ttmt) cc_final: 0.6697 (mttt) REVERT: A 224 VAL cc_start: 0.8807 (p) cc_final: 0.8552 (t) REVERT: A 311 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: A 314 GLU cc_start: 0.7446 (pm20) cc_final: 0.7086 (pm20) REVERT: A 327 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6763 (pp20) REVERT: B 42 ARG cc_start: 0.7033 (ttp-110) cc_final: 0.6590 (ttm110) REVERT: B 46 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.6528 (mpt180) REVERT: B 134 ARG cc_start: 0.6690 (ptm-80) cc_final: 0.6484 (ptt90) REVERT: B 172 GLU cc_start: 0.8018 (tp30) cc_final: 0.7575 (tt0) REVERT: B 209 LYS cc_start: 0.7695 (mttm) cc_final: 0.7453 (mttp) REVERT: B 214 ARG cc_start: 0.7732 (mpt180) cc_final: 0.7352 (mpt180) REVERT: B 243 THR cc_start: 0.8510 (p) cc_final: 0.8174 (p) REVERT: B 254 ASP cc_start: 0.8111 (p0) cc_final: 0.7795 (t0) REVERT: B 325 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7971 (mmt) REVERT: D 8 CYS cc_start: 0.5176 (m) cc_final: 0.4192 (t) REVERT: D 43 ARG cc_start: 0.5743 (mtp180) cc_final: 0.4762 (mtt180) REVERT: D 91 ARG cc_start: 0.5668 (OUTLIER) cc_final: 0.5175 (mtm110) REVERT: D 92 SER cc_start: 0.6542 (p) cc_final: 0.5885 (t) REVERT: D 173 LYS cc_start: 0.6708 (mtpt) cc_final: 0.6163 (tttt) REVERT: D 276 MET cc_start: 0.6353 (mmt) cc_final: 0.5527 (ptp) REVERT: D 307 ARG cc_start: 0.6557 (ttm-80) cc_final: 0.5984 (ttp80) REVERT: N 19 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6789 (tmt90) REVERT: N 65 LYS cc_start: 0.7644 (ttpt) cc_final: 0.6791 (tptt) REVERT: N 89 GLU cc_start: 0.7607 (pp20) cc_final: 0.7195 (pm20) REVERT: N 91 THR cc_start: 0.8109 (t) cc_final: 0.7755 (m) outliers start: 31 outliers final: 14 residues processed: 151 average time/residue: 0.6016 time to fit residues: 96.7479 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 64 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 57 optimal weight: 9.9990 chunk 23 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 239 ASN B 259 GLN 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 = 0.3850 r_free = 0.3850 target = 0.157617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119695 restraints weight = 10386.666| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.58 r_work: 0.3316 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8604 Z= 0.100 Angle : 0.477 7.780 11647 Z= 0.248 Chirality : 0.040 0.155 1313 Planarity : 0.004 0.035 1480 Dihedral : 7.183 92.176 1325 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 3.43 % Allowed : 18.69 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.26), residues: 1046 helix: 3.03 (0.25), residues: 390 sheet: 0.13 (0.34), residues: 201 loop : -0.23 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.011 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.013 0.001 TRP D 182 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8604) covalent geometry : angle 0.47722 (11647) hydrogen bonds : bond 0.03103 ( 406) hydrogen bonds : angle 3.89971 ( 1146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6697 (mt-10) REVERT: A 28 LYS cc_start: 0.7070 (ttmt) cc_final: 0.6682 (mttt) REVERT: A 224 VAL cc_start: 0.8810 (p) cc_final: 0.8600 (t) REVERT: A 314 GLU cc_start: 0.7415 (pm20) cc_final: 0.7136 (pm20) REVERT: A 327 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6757 (pp20) REVERT: B 19 ARG cc_start: 0.7089 (ttm-80) cc_final: 0.6251 (ttp80) REVERT: B 42 ARG cc_start: 0.7000 (ttp-110) cc_final: 0.6518 (ttm110) REVERT: B 46 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.6456 (mpt180) REVERT: B 134 ARG cc_start: 0.6677 (ptm-80) cc_final: 0.6475 (ptt90) REVERT: B 172 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: B 209 LYS cc_start: 0.7657 (mttm) cc_final: 0.7423 (mttp) REVERT: B 214 ARG cc_start: 0.7748 (mpt180) cc_final: 0.7337 (mpt180) REVERT: B 243 THR cc_start: 0.8479 (p) cc_final: 0.8153 (p) REVERT: B 254 ASP cc_start: 0.8091 (p0) cc_final: 0.7743 (t0) REVERT: B 325 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7926 (mmt) REVERT: D 8 CYS cc_start: 0.5061 (m) cc_final: 0.3956 (t) REVERT: D 11 THR cc_start: 0.7395 (m) cc_final: 0.7035 (p) REVERT: D 22 MET cc_start: 0.5039 (OUTLIER) cc_final: 0.4678 (tpp) REVERT: D 43 ARG cc_start: 0.5744 (mtp180) cc_final: 0.4720 (mtt180) REVERT: D 91 ARG cc_start: 0.5598 (OUTLIER) cc_final: 0.5154 (mtm110) REVERT: D 92 SER cc_start: 0.6584 (p) cc_final: 0.5906 (t) REVERT: D 173 LYS cc_start: 0.6667 (mtpt) cc_final: 0.6149 (tttt) REVERT: D 276 MET cc_start: 0.6333 (mmt) cc_final: 0.5473 (ptp) REVERT: D 307 ARG cc_start: 0.6523 (ttm-80) cc_final: 0.5959 (ttp80) REVERT: N 65 LYS cc_start: 0.7577 (ttpt) cc_final: 0.6731 (tptm) REVERT: N 89 GLU cc_start: 0.7630 (pp20) cc_final: 0.7185 (pm20) REVERT: N 91 THR cc_start: 0.8076 (t) cc_final: 0.7722 (m) outliers start: 31 outliers final: 18 residues processed: 150 average time/residue: 0.5923 time to fit residues: 94.5090 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain N residue 64 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 259 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.157021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119035 restraints weight = 10274.365| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.58 r_work: 0.3305 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8604 Z= 0.109 Angle : 0.482 6.486 11647 Z= 0.251 Chirality : 0.040 0.150 1313 Planarity : 0.004 0.034 1480 Dihedral : 7.223 93.900 1325 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 3.32 % Allowed : 18.92 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.26), residues: 1046 helix: 3.03 (0.25), residues: 390 sheet: 0.25 (0.33), residues: 210 loop : -0.24 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 19 TYR 0.011 0.001 TYR N 80 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8604) covalent geometry : angle 0.48235 (11647) hydrogen bonds : bond 0.03213 ( 406) hydrogen bonds : angle 3.90205 ( 1146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6757 (mt-10) REVERT: A 28 LYS cc_start: 0.7101 (ttmt) cc_final: 0.6696 (mttt) REVERT: A 61 ARG cc_start: 0.6633 (mtm-85) cc_final: 0.6381 (mtt180) REVERT: A 224 VAL cc_start: 0.8787 (p) cc_final: 0.8581 (t) REVERT: A 314 GLU cc_start: 0.7419 (pm20) cc_final: 0.7121 (pm20) REVERT: A 327 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6768 (pp20) REVERT: B 19 ARG cc_start: 0.7099 (ttm-80) cc_final: 0.6264 (ttp80) REVERT: B 42 ARG cc_start: 0.7009 (ttp-110) cc_final: 0.6546 (ttm110) REVERT: B 46 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.6497 (mpt180) REVERT: B 118 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7627 (p0) REVERT: B 134 ARG cc_start: 0.6690 (ptm-80) cc_final: 0.6482 (ptt90) REVERT: B 172 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: B 209 LYS cc_start: 0.7694 (mttm) cc_final: 0.7452 (mttp) REVERT: B 214 ARG cc_start: 0.7745 (mpt180) cc_final: 0.7317 (mpt180) REVERT: B 243 THR cc_start: 0.8488 (p) cc_final: 0.8161 (p) REVERT: B 254 ASP cc_start: 0.8071 (p0) cc_final: 0.7738 (t0) REVERT: B 325 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8019 (mmt) REVERT: D 8 CYS cc_start: 0.5011 (m) cc_final: 0.3926 (t) REVERT: D 11 THR cc_start: 0.7328 (m) cc_final: 0.6977 (p) REVERT: D 22 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.4716 (tpp) REVERT: D 43 ARG cc_start: 0.5728 (mtp180) cc_final: 0.4704 (mtt180) REVERT: D 91 ARG cc_start: 0.5618 (OUTLIER) cc_final: 0.5175 (mtm110) REVERT: D 92 SER cc_start: 0.6629 (p) cc_final: 0.5941 (t) REVERT: D 173 LYS cc_start: 0.6704 (mtpt) cc_final: 0.6170 (ttpt) REVERT: D 183 CYS cc_start: 0.8275 (m) cc_final: 0.7918 (p) REVERT: D 276 MET cc_start: 0.6444 (mmt) cc_final: 0.5556 (ptp) REVERT: D 307 ARG cc_start: 0.6579 (ttm-80) cc_final: 0.6016 (ttp80) REVERT: N 65 LYS cc_start: 0.7595 (ttpt) cc_final: 0.6739 (tptm) REVERT: N 89 GLU cc_start: 0.7686 (pp20) cc_final: 0.7230 (pm20) REVERT: N 91 THR cc_start: 0.8076 (t) cc_final: 0.7705 (m) outliers start: 30 outliers final: 21 residues processed: 146 average time/residue: 0.5326 time to fit residues: 83.1589 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain N residue 64 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 84 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 0.0470 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 259 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.157725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120045 restraints weight = 10367.283| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.59 r_work: 0.3321 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8604 Z= 0.100 Angle : 0.469 6.198 11647 Z= 0.245 Chirality : 0.040 0.153 1313 Planarity : 0.003 0.035 1480 Dihedral : 6.988 92.203 1325 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.54 % Allowed : 18.92 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.26), residues: 1046 helix: 3.06 (0.25), residues: 390 sheet: 0.30 (0.33), residues: 210 loop : -0.25 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.010 0.001 TYR N 80 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP A 234 HIS 0.002 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8604) covalent geometry : angle 0.46864 (11647) hydrogen bonds : bond 0.03087 ( 406) hydrogen bonds : angle 3.85733 ( 1146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6710 (mt-10) REVERT: A 28 LYS cc_start: 0.7110 (ttmt) cc_final: 0.6755 (mttt) REVERT: A 61 ARG cc_start: 0.6641 (mtm-85) cc_final: 0.6392 (mtt180) REVERT: A 314 GLU cc_start: 0.7420 (pm20) cc_final: 0.7122 (pm20) REVERT: A 327 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6766 (pp20) REVERT: B 19 ARG cc_start: 0.7109 (ttm-80) cc_final: 0.6268 (ttp80) REVERT: B 42 ARG cc_start: 0.6964 (ttp-110) cc_final: 0.6453 (ttm110) REVERT: B 46 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.6521 (mpt180) REVERT: B 118 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7618 (p0) REVERT: B 134 ARG cc_start: 0.6724 (ptm-80) cc_final: 0.6522 (ptt90) REVERT: B 172 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: B 209 LYS cc_start: 0.7667 (mttm) cc_final: 0.7441 (mttp) REVERT: B 214 ARG cc_start: 0.7771 (mpt180) cc_final: 0.7331 (mpt180) REVERT: B 243 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8159 (p) REVERT: B 254 ASP cc_start: 0.8065 (p0) cc_final: 0.7734 (t0) REVERT: B 325 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7958 (mmt) REVERT: D 8 CYS cc_start: 0.4825 (m) cc_final: 0.3766 (t) REVERT: D 11 THR cc_start: 0.7374 (m) cc_final: 0.7022 (p) REVERT: D 22 MET cc_start: 0.5142 (OUTLIER) cc_final: 0.4604 (tpp) REVERT: D 43 ARG cc_start: 0.5769 (mtp180) cc_final: 0.4743 (mtt180) REVERT: D 91 ARG cc_start: 0.5687 (OUTLIER) cc_final: 0.5427 (mtm110) REVERT: D 92 SER cc_start: 0.6660 (p) cc_final: 0.6018 (t) REVERT: D 173 LYS cc_start: 0.6654 (mtpt) cc_final: 0.6197 (tttt) REVERT: D 276 MET cc_start: 0.6459 (mmt) cc_final: 0.5584 (ptp) REVERT: D 307 ARG cc_start: 0.6585 (ttm-80) cc_final: 0.6015 (ttp80) REVERT: N 43 LYS cc_start: 0.7434 (ttmm) cc_final: 0.6885 (mmtt) REVERT: N 65 LYS cc_start: 0.7560 (ttpt) cc_final: 0.6728 (tptm) REVERT: N 89 GLU cc_start: 0.7712 (pp20) cc_final: 0.7399 (pp20) REVERT: N 91 THR cc_start: 0.8076 (t) cc_final: 0.7687 (m) outliers start: 32 outliers final: 19 residues processed: 151 average time/residue: 0.5920 time to fit residues: 95.2118 Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain N residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 78 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 0.0570 chunk 46 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 259 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120439 restraints weight = 10338.603| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.58 r_work: 0.3338 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8604 Z= 0.100 Angle : 0.473 6.406 11647 Z= 0.246 Chirality : 0.039 0.158 1313 Planarity : 0.003 0.035 1480 Dihedral : 6.902 94.340 1325 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.65 % Allowed : 19.14 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.26), residues: 1046 helix: 3.05 (0.25), residues: 390 sheet: 0.36 (0.34), residues: 208 loop : -0.23 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 19 TYR 0.010 0.001 TYR D 287 PHE 0.012 0.001 PHE B 199 TRP 0.017 0.001 TRP A 234 HIS 0.003 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8604) covalent geometry : angle 0.47285 (11647) hydrogen bonds : bond 0.03065 ( 406) hydrogen bonds : angle 3.88086 ( 1146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6715 (mt-10) REVERT: A 28 LYS cc_start: 0.7131 (ttmt) cc_final: 0.6774 (mttt) REVERT: A 61 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6471 (mtt180) REVERT: A 314 GLU cc_start: 0.7422 (pm20) cc_final: 0.7086 (pm20) REVERT: A 327 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6781 (pp20) REVERT: B 19 ARG cc_start: 0.7138 (ttm-80) cc_final: 0.6297 (ttp80) REVERT: B 42 ARG cc_start: 0.6948 (ttp-110) cc_final: 0.6456 (ttm110) REVERT: B 46 ARG cc_start: 0.7964 (mtp-110) cc_final: 0.6562 (mpt180) REVERT: B 118 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7651 (p0) REVERT: B 134 ARG cc_start: 0.6734 (ptm-80) cc_final: 0.6533 (ptt90) REVERT: B 172 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: B 209 LYS cc_start: 0.7686 (mttm) cc_final: 0.7449 (mttp) REVERT: B 214 ARG cc_start: 0.7763 (mpt180) cc_final: 0.7337 (mpt180) REVERT: B 243 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8155 (p) REVERT: B 254 ASP cc_start: 0.8064 (p0) cc_final: 0.7729 (t0) REVERT: B 325 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7977 (mmt) REVERT: D 8 CYS cc_start: 0.4794 (m) cc_final: 0.3738 (t) REVERT: D 11 THR cc_start: 0.7410 (m) cc_final: 0.7133 (p) REVERT: D 22 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.4642 (tpp) REVERT: D 43 ARG cc_start: 0.5781 (mtp180) cc_final: 0.4744 (mtt180) REVERT: D 91 ARG cc_start: 0.5717 (OUTLIER) cc_final: 0.5292 (mtm110) REVERT: D 92 SER cc_start: 0.6649 (p) cc_final: 0.5946 (t) REVERT: D 173 LYS cc_start: 0.6693 (mtpt) cc_final: 0.6234 (tttt) REVERT: D 190 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: D 276 MET cc_start: 0.6500 (mmt) cc_final: 0.5632 (ptp) REVERT: D 307 ARG cc_start: 0.6595 (ttm-80) cc_final: 0.6019 (ttp80) REVERT: N 43 LYS cc_start: 0.7428 (ttmm) cc_final: 0.6891 (mmtt) REVERT: N 65 LYS cc_start: 0.7548 (ttpt) cc_final: 0.6728 (tptt) REVERT: N 89 GLU cc_start: 0.7731 (pp20) cc_final: 0.7421 (pp20) REVERT: N 91 THR cc_start: 0.8070 (t) cc_final: 0.7679 (m) outliers start: 33 outliers final: 17 residues processed: 152 average time/residue: 0.6024 time to fit residues: 97.5706 Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain N residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 60 optimal weight: 0.0270 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 259 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119775 restraints weight = 10384.103| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.70 r_work: 0.3334 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8604 Z= 0.097 Angle : 0.475 8.393 11647 Z= 0.245 Chirality : 0.040 0.160 1313 Planarity : 0.004 0.035 1480 Dihedral : 6.691 92.955 1325 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.32 % Allowed : 19.69 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.26), residues: 1046 helix: 3.08 (0.25), residues: 390 sheet: 0.39 (0.34), residues: 209 loop : -0.25 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 19 TYR 0.011 0.001 TYR N 80 PHE 0.012 0.001 PHE B 199 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8604) covalent geometry : angle 0.47463 (11647) hydrogen bonds : bond 0.03023 ( 406) hydrogen bonds : angle 3.86947 ( 1146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.60 seconds wall clock time: 54 minutes 37.20 seconds (3277.20 seconds total)