Starting phenix.real_space_refine on Sat Jun 7 01:57:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zw0_60514/06_2025/8zw0_60514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zw0_60514/06_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_60514/06_2025/8zw0_60514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zw0_60514/06_2025/8zw0_60514.map" model { file = "/net/cci-nas-00/data/ceres_data/8zw0_60514/06_2025/8zw0_60514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zw0_60514/06_2025/8zw0_60514.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.86, per 1000 atoms: 0.70 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.03 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: 2.35 Time building geometry restraints manager: 2.74 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: 1.960 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.280 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.470 ------------------------------------------------------------------------------- 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 : 7.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (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 TRP 0.004 0.000 TRP A 234 HIS 0.005 0.000 HIS D 189 PHE 0.005 0.000 PHE D 290 TYR 0.005 0.001 TYR D 87 ARG 0.002 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.17710 ( 406) hydrogen bonds : angle 6.60118 ( 1146) covalent geometry : bond 0.00538 ( 8604) covalent geometry : angle 0.73228 (11647) *********************** 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 : 0.853 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: 1.1080 time to fit residues: 278.0536 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 : 0.987 ------------------------------------------------------------------------------- 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 86 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 52 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.0170 chunk 93 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.168924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131386 restraints weight = 10295.801| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.61 r_work: 0.3476 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8604 Z= 0.125 Angle : 0.569 7.840 11647 Z= 0.292 Chirality : 0.043 0.183 1313 Planarity : 0.004 0.032 1480 Dihedral : 8.242 99.013 1338 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 4.09 % Allowed : 13.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1046 helix: 2.12 (0.26), residues: 396 sheet: -0.41 (0.35), residues: 203 loop : -0.67 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS D 235 PHE 0.010 0.001 PHE D 290 TYR 0.014 0.001 TYR N 80 ARG 0.005 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 406) hydrogen bonds : angle 4.41881 ( 1146) covalent geometry : bond 0.00280 ( 8604) covalent geometry : angle 0.56899 (11647) *********************** 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 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6223 (mt-10) REVERT: A 314 GLU cc_start: 0.7353 (pm20) cc_final: 0.7082 (pm20) REVERT: B 46 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7320 (mtp180) REVERT: B 124 TYR cc_start: 0.7614 (m-80) cc_final: 0.7363 (m-80) REVERT: B 139 LEU cc_start: 0.6111 (mt) cc_final: 0.5790 (mt) REVERT: B 172 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7635 (tp30) REVERT: B 209 LYS cc_start: 0.7418 (mttm) cc_final: 0.7111 (mttp) REVERT: B 215 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: B 237 ASN cc_start: 0.7573 (t0) cc_final: 0.7322 (p0) REVERT: B 243 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8274 (p) REVERT: B 254 ASP cc_start: 0.7807 (p0) cc_final: 0.7441 (p0) REVERT: D 9 GLN cc_start: 0.6259 (tt0) cc_final: 0.5583 (tp40) REVERT: D 11 THR cc_start: 0.7596 (m) cc_final: 0.7350 (p) REVERT: D 22 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.6047 (tpp) REVERT: D 43 ARG cc_start: 0.6004 (mtp180) cc_final: 0.4995 (mtt180) REVERT: D 74 LEU cc_start: 0.7147 (mt) cc_final: 0.6913 (mm) REVERT: D 95 VAL cc_start: 0.7212 (m) cc_final: 0.6487 (p) REVERT: D 169 MET cc_start: 0.6951 (mtt) cc_final: 0.6748 (ptp) REVERT: D 173 LYS cc_start: 0.5992 (mtpt) cc_final: 0.5539 (tttt) REVERT: D 276 MET cc_start: 0.6427 (mmt) cc_final: 0.5631 (ptp) REVERT: N 82 GLN cc_start: 0.7561 (tp40) cc_final: 0.7256 (tp40) REVERT: N 89 GLU cc_start: 0.7327 (pp20) cc_final: 0.6997 (pm20) REVERT: N 91 THR cc_start: 0.8115 (t) cc_final: 0.7804 (m) REVERT: N 93 VAL cc_start: 0.8138 (m) cc_final: 0.7935 (p) outliers start: 37 outliers final: 10 residues processed: 163 average time/residue: 1.0482 time to fit residues: 184.1295 Evaluate side-chains 140 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 61 MET 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 161 LEU Chi-restraints excluded: chain D residue 190 GLU 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 49 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 259 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119754 restraints weight = 10502.472| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.63 r_work: 0.3379 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8604 Z= 0.159 Angle : 0.578 10.412 11647 Z= 0.297 Chirality : 0.043 0.202 1313 Planarity : 0.004 0.041 1480 Dihedral : 8.090 100.688 1327 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.94 % Rotamer: Outliers : 4.20 % Allowed : 14.71 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1046 helix: 2.49 (0.26), residues: 388 sheet: -0.17 (0.35), residues: 199 loop : -0.53 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.002 HIS D 235 PHE 0.021 0.002 PHE D 5 TYR 0.013 0.002 TYR N 80 ARG 0.004 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 406) hydrogen bonds : angle 4.31149 ( 1146) covalent geometry : bond 0.00380 ( 8604) covalent geometry : angle 0.57758 (11647) *********************** 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 179 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6965 (mt-10) REVERT: A 28 LYS cc_start: 0.7225 (ttmt) cc_final: 0.6850 (mttt) REVERT: A 29 GLN cc_start: 0.6963 (tp40) cc_final: 0.6732 (mm-40) REVERT: A 311 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6670 (m-80) REVERT: A 314 GLU cc_start: 0.7646 (pm20) cc_final: 0.7337 (pm20) REVERT: B 78 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8217 (tppt) REVERT: B 134 ARG cc_start: 0.6909 (ptm-80) cc_final: 0.6663 (ptt90) REVERT: B 209 LYS cc_start: 0.8018 (mttm) cc_final: 0.7805 (mttp) REVERT: B 214 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7536 (mtt90) REVERT: B 243 THR cc_start: 0.8699 (p) cc_final: 0.8400 (p) REVERT: B 254 ASP cc_start: 0.8296 (p0) cc_final: 0.7856 (t0) REVERT: D 11 THR cc_start: 0.7634 (m) cc_final: 0.7246 (p) REVERT: D 22 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.6100 (tpp) REVERT: D 43 ARG cc_start: 0.6011 (mtp180) cc_final: 0.4942 (mtt180) REVERT: D 91 ARG cc_start: 0.5913 (mtm-85) cc_final: 0.5573 (mtm-85) REVERT: D 173 LYS cc_start: 0.6684 (mtpt) cc_final: 0.6198 (tttt) REVERT: D 276 MET cc_start: 0.6751 (mmt) cc_final: 0.5899 (ptp) REVERT: D 307 ARG cc_start: 0.6962 (ttm-80) cc_final: 0.6333 (ttm110) REVERT: N 19 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6917 (tmt90) REVERT: N 30 SER cc_start: 0.8868 (p) cc_final: 0.8657 (m) REVERT: N 76 LYS cc_start: 0.7766 (ptpt) cc_final: 0.7562 (ptpp) REVERT: N 89 GLU cc_start: 0.7620 (pp20) cc_final: 0.7241 (pm20) REVERT: N 91 THR cc_start: 0.8327 (t) cc_final: 0.7973 (m) REVERT: N 93 VAL cc_start: 0.8328 (m) cc_final: 0.8074 (p) outliers start: 38 outliers final: 13 residues processed: 162 average time/residue: 1.6816 time to fit residues: 291.7707 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 267 ASP 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 259 GLN D 9 GLN D 106 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 = 0.3892 r_free = 0.3892 target = 0.158909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120259 restraints weight = 10338.161| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.59 r_work: 0.3391 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4167 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= 0.133 Angle : 0.521 7.640 11647 Z= 0.270 Chirality : 0.041 0.224 1313 Planarity : 0.004 0.036 1480 Dihedral : 7.784 99.779 1325 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 4.54 % Allowed : 16.04 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1046 helix: 2.71 (0.25), residues: 390 sheet: -0.14 (0.35), residues: 199 loop : -0.42 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS B 183 PHE 0.013 0.001 PHE B 199 TYR 0.010 0.001 TYR A 339 ARG 0.006 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 406) hydrogen bonds : angle 4.12885 ( 1146) covalent geometry : bond 0.00316 ( 8604) covalent geometry : angle 0.52092 (11647) *********************** 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 172 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7692 (mm-30) cc_final: 0.6964 (mt-10) REVERT: A 28 LYS cc_start: 0.7192 (ttmt) cc_final: 0.6833 (mttt) REVERT: A 224 VAL cc_start: 0.8919 (p) cc_final: 0.8573 (t) REVERT: A 314 GLU cc_start: 0.7516 (pm20) cc_final: 0.7208 (pm20) REVERT: B 46 ARG cc_start: 0.7934 (mtp-110) cc_final: 0.6534 (mpt180) REVERT: B 59 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: B 134 ARG cc_start: 0.6844 (ptm-80) cc_final: 0.6622 (ptt90) REVERT: B 172 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: B 209 LYS cc_start: 0.7941 (mttm) cc_final: 0.7713 (mttp) REVERT: B 214 ARG cc_start: 0.7846 (mtt90) cc_final: 0.7409 (mtt90) REVERT: B 243 THR cc_start: 0.8688 (p) cc_final: 0.8390 (p) REVERT: B 254 ASP cc_start: 0.8307 (p0) cc_final: 0.7945 (t70) REVERT: D 11 THR cc_start: 0.7493 (m) cc_final: 0.7091 (p) REVERT: D 22 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.6001 (tpp) REVERT: D 43 ARG cc_start: 0.5949 (mtp180) cc_final: 0.4954 (mtt180) REVERT: D 173 LYS cc_start: 0.6711 (mtpt) cc_final: 0.6167 (tttt) REVERT: D 276 MET cc_start: 0.6688 (mmt) cc_final: 0.5786 (ptp) REVERT: D 307 ARG cc_start: 0.6814 (ttm-80) cc_final: 0.6167 (ttp80) REVERT: N 19 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6770 (tmt90) REVERT: N 30 SER cc_start: 0.8886 (p) cc_final: 0.8678 (m) REVERT: N 89 GLU cc_start: 0.7600 (pp20) cc_final: 0.7244 (pm20) REVERT: N 91 THR cc_start: 0.8206 (t) cc_final: 0.7860 (m) REVERT: N 93 VAL cc_start: 0.8231 (m) cc_final: 0.7982 (p) outliers start: 41 outliers final: 16 residues processed: 157 average time/residue: 1.0831 time to fit residues: 182.1145 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS 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 D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET 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 Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 18 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 237 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118308 restraints weight = 10197.173| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.56 r_work: 0.3317 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4364 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= 0.124 Angle : 0.512 7.856 11647 Z= 0.265 Chirality : 0.041 0.190 1313 Planarity : 0.004 0.048 1480 Dihedral : 7.632 95.379 1325 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.51 % Rotamer: Outliers : 3.87 % Allowed : 17.04 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1046 helix: 2.85 (0.25), residues: 391 sheet: -0.09 (0.35), residues: 197 loop : -0.30 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR A 339 ARG 0.007 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 406) hydrogen bonds : angle 4.03628 ( 1146) covalent geometry : bond 0.00291 ( 8604) covalent geometry : angle 0.51175 (11647) *********************** 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 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6873 (mt-10) REVERT: A 28 LYS cc_start: 0.7142 (ttmt) cc_final: 0.6770 (mttp) REVERT: A 224 VAL cc_start: 0.8856 (p) cc_final: 0.8566 (t) REVERT: A 311 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: A 314 GLU cc_start: 0.7494 (pm20) cc_final: 0.7147 (pm20) REVERT: B 46 ARG cc_start: 0.7815 (mtp180) cc_final: 0.6388 (mpt180) REVERT: B 118 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7784 (p0) REVERT: B 172 GLU cc_start: 0.7964 (tp30) cc_final: 0.7558 (tt0) REVERT: B 209 LYS cc_start: 0.7845 (mttm) cc_final: 0.7613 (mttp) REVERT: B 243 THR cc_start: 0.8602 (p) cc_final: 0.8291 (p) REVERT: B 254 ASP cc_start: 0.8268 (p0) cc_final: 0.7899 (t0) REVERT: B 336 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8464 (mp) REVERT: D 11 THR cc_start: 0.7272 (m) cc_final: 0.6843 (p) REVERT: D 22 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5752 (tpp) REVERT: D 43 ARG cc_start: 0.5758 (mtp180) cc_final: 0.4780 (mtt180) REVERT: D 91 ARG cc_start: 0.5712 (mtm-85) cc_final: 0.5370 (mtm110) REVERT: D 173 LYS cc_start: 0.6761 (mtpt) cc_final: 0.6223 (tttt) REVERT: D 276 MET cc_start: 0.6482 (mmt) cc_final: 0.5600 (ptp) REVERT: D 307 ARG cc_start: 0.6674 (ttm-80) cc_final: 0.6096 (ttp80) REVERT: N 19 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6673 (tmt90) REVERT: N 65 LYS cc_start: 0.7711 (ttpt) cc_final: 0.6850 (tptm) REVERT: N 89 GLU cc_start: 0.7629 (pp20) cc_final: 0.7247 (pm20) REVERT: N 91 THR cc_start: 0.8111 (t) cc_final: 0.7750 (m) outliers start: 35 outliers final: 18 residues processed: 155 average time/residue: 1.0908 time to fit residues: 181.1234 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL 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 78 LYS 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 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET 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 18 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 0.0270 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 0.0870 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 237 ASN B 259 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.158187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119031 restraints weight = 10311.641| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.67 r_work: 0.3327 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8604 Z= 0.103 Angle : 0.479 6.883 11647 Z= 0.249 Chirality : 0.040 0.161 1313 Planarity : 0.004 0.035 1480 Dihedral : 7.405 93.566 1325 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.32 % Rotamer: Outliers : 4.09 % Allowed : 17.15 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.26), residues: 1046 helix: 3.00 (0.25), residues: 390 sheet: -0.02 (0.35), residues: 202 loop : -0.23 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 220 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR N 95 ARG 0.005 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 406) hydrogen bonds : angle 3.94005 ( 1146) covalent geometry : bond 0.00234 ( 8604) covalent geometry : angle 0.47946 (11647) *********************** 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 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6695 (mt-10) REVERT: A 28 LYS cc_start: 0.7096 (ttmt) cc_final: 0.6700 (mttt) REVERT: A 61 ARG cc_start: 0.6854 (mtm-85) cc_final: 0.6060 (mtt-85) REVERT: A 224 VAL cc_start: 0.8823 (p) cc_final: 0.8578 (t) REVERT: A 314 GLU cc_start: 0.7459 (pm20) cc_final: 0.7109 (pm20) REVERT: B 46 ARG cc_start: 0.7712 (mtp180) cc_final: 0.6286 (mpt180) REVERT: B 118 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7630 (p0) REVERT: B 172 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: B 209 LYS cc_start: 0.7700 (mttm) cc_final: 0.7457 (mttp) REVERT: B 214 ARG cc_start: 0.7764 (mpt90) cc_final: 0.7433 (mpt90) REVERT: B 243 THR cc_start: 0.8473 (p) cc_final: 0.8156 (p) REVERT: B 254 ASP cc_start: 0.8100 (p0) cc_final: 0.7770 (t0) REVERT: B 336 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8418 (mp) REVERT: D 8 CYS cc_start: 0.4919 (m) cc_final: 0.3739 (t) REVERT: D 11 THR cc_start: 0.7333 (m) cc_final: 0.6712 (p) REVERT: D 43 ARG cc_start: 0.5811 (mtp180) cc_final: 0.4734 (mtt180) REVERT: D 91 ARG cc_start: 0.5699 (mtm-85) cc_final: 0.5349 (mtm110) REVERT: D 173 LYS cc_start: 0.6677 (mtpt) cc_final: 0.6169 (tttt) REVERT: D 276 MET cc_start: 0.6383 (mmt) cc_final: 0.5569 (ptp) REVERT: D 307 ARG cc_start: 0.6559 (ttm-80) cc_final: 0.6000 (ttp80) REVERT: N 19 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6747 (tmt90) REVERT: N 65 LYS cc_start: 0.7607 (ttpt) cc_final: 0.6754 (tptm) REVERT: N 73 ASP cc_start: 0.7525 (p0) cc_final: 0.7274 (p0) REVERT: N 89 GLU cc_start: 0.7651 (pp20) cc_final: 0.7251 (pm20) REVERT: N 91 THR cc_start: 0.8111 (t) cc_final: 0.7759 (m) outliers start: 37 outliers final: 20 residues processed: 153 average time/residue: 1.1552 time to fit residues: 188.7649 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 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 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 14 VAL 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 19 ARG Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.0270 chunk 90 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 75 GLN B 237 ASN B 259 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119985 restraints weight = 10285.202| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.56 r_work: 0.3322 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4574 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= 0.104 Angle : 0.481 7.926 11647 Z= 0.248 Chirality : 0.040 0.152 1313 Planarity : 0.004 0.035 1480 Dihedral : 7.199 92.757 1325 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.87 % Allowed : 17.92 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1046 helix: 3.08 (0.25), residues: 390 sheet: 0.07 (0.35), residues: 201 loop : -0.23 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS D 235 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.004 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 406) hydrogen bonds : angle 3.87901 ( 1146) covalent geometry : bond 0.00239 ( 8604) covalent geometry : angle 0.48104 (11647) *********************** 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 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6732 (mt-10) REVERT: A 28 LYS cc_start: 0.7085 (ttmt) cc_final: 0.6679 (mttt) REVERT: A 61 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.6558 (mtt180) REVERT: A 224 VAL cc_start: 0.8796 (p) cc_final: 0.8588 (t) REVERT: A 314 GLU cc_start: 0.7425 (pm20) cc_final: 0.7153 (pm20) REVERT: B 46 ARG cc_start: 0.7709 (mtp180) cc_final: 0.6292 (mpt180) REVERT: B 59 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: B 78 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7803 (tppt) REVERT: B 118 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7591 (p0) REVERT: B 172 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: B 209 LYS cc_start: 0.7611 (mttm) cc_final: 0.7386 (mttp) REVERT: B 214 ARG cc_start: 0.7791 (mpt90) cc_final: 0.7401 (mpt90) REVERT: B 243 THR cc_start: 0.8452 (p) cc_final: 0.8136 (p) REVERT: B 254 ASP cc_start: 0.8065 (p0) cc_final: 0.7733 (t0) REVERT: B 336 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8391 (mp) REVERT: D 11 THR cc_start: 0.7300 (m) cc_final: 0.6997 (p) REVERT: D 22 MET cc_start: 0.5059 (OUTLIER) cc_final: 0.4691 (tpp) REVERT: D 43 ARG cc_start: 0.5739 (mtp180) cc_final: 0.4723 (mtt180) REVERT: D 91 ARG cc_start: 0.5705 (mtm-85) cc_final: 0.5285 (mtm110) REVERT: D 92 SER cc_start: 0.6499 (p) cc_final: 0.5862 (t) REVERT: D 173 LYS cc_start: 0.6662 (mtpt) cc_final: 0.6133 (ttpt) REVERT: D 276 MET cc_start: 0.6409 (mmt) cc_final: 0.5584 (ptp) REVERT: D 307 ARG cc_start: 0.6549 (ttm-80) cc_final: 0.5991 (ttp80) REVERT: N 19 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6695 (tmt90) REVERT: N 43 LYS cc_start: 0.7475 (ttmm) cc_final: 0.6823 (mmtt) REVERT: N 65 LYS cc_start: 0.7580 (ttpt) cc_final: 0.6734 (tptt) REVERT: N 89 GLU cc_start: 0.7681 (pp20) cc_final: 0.7261 (pm20) REVERT: N 91 THR cc_start: 0.8081 (t) cc_final: 0.7714 (m) outliers start: 35 outliers final: 18 residues processed: 155 average time/residue: 1.0628 time to fit residues: 176.8191 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 372 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 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 267 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU 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 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 19 ARG 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 31 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 0.1980 chunk 101 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 237 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 = 0.3854 r_free = 0.3854 target = 0.157848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120224 restraints weight = 10338.617| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.57 r_work: 0.3335 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8604 Z= 0.103 Angle : 0.476 6.064 11647 Z= 0.246 Chirality : 0.040 0.156 1313 Planarity : 0.003 0.035 1480 Dihedral : 7.100 93.463 1325 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.31 % Allowed : 18.03 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1046 helix: 3.08 (0.25), residues: 390 sheet: 0.12 (0.35), residues: 202 loop : -0.21 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 182 HIS 0.003 0.001 HIS D 235 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.004 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 406) hydrogen bonds : angle 3.90830 ( 1146) covalent geometry : bond 0.00239 ( 8604) covalent geometry : angle 0.47574 (11647) *********************** 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 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6759 (mt-10) REVERT: A 28 LYS cc_start: 0.7113 (ttmt) cc_final: 0.6764 (mttt) REVERT: A 61 ARG cc_start: 0.6970 (mtm-85) cc_final: 0.6715 (mtt180) REVERT: A 327 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6745 (pp20) REVERT: B 46 ARG cc_start: 0.7733 (mtp180) cc_final: 0.6326 (mpt180) REVERT: B 78 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7817 (tppt) REVERT: B 118 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7608 (p0) REVERT: B 172 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: B 209 LYS cc_start: 0.7651 (mttm) cc_final: 0.7410 (mttp) REVERT: B 214 ARG cc_start: 0.7817 (mpt90) cc_final: 0.7088 (mpt180) REVERT: B 243 THR cc_start: 0.8472 (p) cc_final: 0.8149 (p) REVERT: B 254 ASP cc_start: 0.8070 (p0) cc_final: 0.7746 (t0) REVERT: B 336 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8377 (mp) REVERT: D 8 CYS cc_start: 0.4826 (m) cc_final: 0.3680 (t) REVERT: D 11 THR cc_start: 0.7314 (m) cc_final: 0.6774 (p) REVERT: D 22 MET cc_start: 0.5078 (OUTLIER) cc_final: 0.4683 (tpp) REVERT: D 43 ARG cc_start: 0.5719 (mtp180) cc_final: 0.4689 (mtt180) REVERT: D 91 ARG cc_start: 0.5747 (mtm-85) cc_final: 0.5349 (mtm110) REVERT: D 92 SER cc_start: 0.6519 (p) cc_final: 0.5843 (t) REVERT: D 173 LYS cc_start: 0.6661 (mtpt) cc_final: 0.6134 (ttpt) REVERT: D 183 CYS cc_start: 0.8235 (m) cc_final: 0.7966 (p) REVERT: D 276 MET cc_start: 0.6486 (mmt) cc_final: 0.5619 (ptp) REVERT: D 307 ARG cc_start: 0.6555 (ttm-80) cc_final: 0.6005 (ttp80) REVERT: N 43 LYS cc_start: 0.7474 (ttmm) cc_final: 0.6897 (mmtt) REVERT: N 65 LYS cc_start: 0.7577 (ttpt) cc_final: 0.6765 (tptm) REVERT: N 89 GLU cc_start: 0.7735 (pp20) cc_final: 0.7291 (pm20) REVERT: N 91 THR cc_start: 0.8073 (t) cc_final: 0.7714 (m) outliers start: 39 outliers final: 21 residues processed: 150 average time/residue: 1.1208 time to fit residues: 180.6072 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 310 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 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 267 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET 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 61 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 78 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117534 restraints weight = 10354.846| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.57 r_work: 0.3304 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8604 Z= 0.125 Angle : 0.497 6.300 11647 Z= 0.258 Chirality : 0.040 0.150 1313 Planarity : 0.004 0.035 1480 Dihedral : 7.038 95.992 1325 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.32 % Allowed : 19.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1046 helix: 2.99 (0.25), residues: 390 sheet: 0.10 (0.35), residues: 205 loop : -0.27 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.003 0.001 HIS D 235 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.006 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 406) hydrogen bonds : angle 3.99393 ( 1146) covalent geometry : bond 0.00297 ( 8604) covalent geometry : angle 0.49691 (11647) *********************** 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 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6777 (mt-10) REVERT: A 28 LYS cc_start: 0.7109 (ttmt) cc_final: 0.6760 (mttt) REVERT: A 61 ARG cc_start: 0.6919 (mtm-85) cc_final: 0.6555 (mtt180) REVERT: A 327 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6792 (pp20) REVERT: B 19 ARG cc_start: 0.7092 (ttm-80) cc_final: 0.6256 (ttp80) REVERT: B 46 ARG cc_start: 0.7780 (mtp180) cc_final: 0.6378 (mpt180) REVERT: B 118 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7659 (p0) REVERT: B 172 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: B 209 LYS cc_start: 0.7746 (mttm) cc_final: 0.7502 (mttp) REVERT: B 214 ARG cc_start: 0.7862 (mpt90) cc_final: 0.7091 (mpt180) REVERT: B 254 ASP cc_start: 0.8048 (p0) cc_final: 0.7763 (t0) REVERT: B 336 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8381 (mp) REVERT: D 11 THR cc_start: 0.7283 (m) cc_final: 0.6931 (p) REVERT: D 22 MET cc_start: 0.5168 (OUTLIER) cc_final: 0.4626 (tpp) REVERT: D 43 ARG cc_start: 0.5706 (mtp180) cc_final: 0.4693 (mtt180) REVERT: D 91 ARG cc_start: 0.5707 (mtm-85) cc_final: 0.5344 (mtm110) REVERT: D 92 SER cc_start: 0.6665 (p) cc_final: 0.6100 (p) REVERT: D 173 LYS cc_start: 0.6728 (mtpt) cc_final: 0.6188 (ttpt) REVERT: D 183 CYS cc_start: 0.8307 (m) cc_final: 0.7884 (p) REVERT: D 276 MET cc_start: 0.6426 (mmt) cc_final: 0.5615 (ptp) REVERT: D 307 ARG cc_start: 0.6588 (ttm-80) cc_final: 0.6038 (ttp80) REVERT: N 43 LYS cc_start: 0.7500 (ttmm) cc_final: 0.6933 (mmtt) REVERT: N 65 LYS cc_start: 0.7619 (ttpt) cc_final: 0.6792 (tptm) REVERT: N 89 GLU cc_start: 0.7868 (pp20) cc_final: 0.7432 (pm20) REVERT: N 91 THR cc_start: 0.8102 (t) cc_final: 0.7729 (m) outliers start: 30 outliers final: 20 residues processed: 146 average time/residue: 1.1307 time to fit residues: 176.6178 Evaluate side-chains 143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 310 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 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 267 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 146 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 237 ASN B 259 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116155 restraints weight = 10419.407| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.68 r_work: 0.3297 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4846 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 : 0.494 6.166 11647 Z= 0.257 Chirality : 0.040 0.158 1313 Planarity : 0.004 0.035 1480 Dihedral : 6.940 95.749 1325 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.21 % Allowed : 19.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1046 helix: 2.96 (0.25), residues: 390 sheet: 0.14 (0.34), residues: 213 loop : -0.29 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS D 235 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR N 80 ARG 0.005 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 406) hydrogen bonds : angle 3.99544 ( 1146) covalent geometry : bond 0.00295 ( 8604) covalent geometry : angle 0.49438 (11647) ********************** 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 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6800 (mt-10) REVERT: A 28 LYS cc_start: 0.7130 (ttmt) cc_final: 0.6777 (mttt) REVERT: A 61 ARG cc_start: 0.6938 (mtm-85) cc_final: 0.6580 (mtt180) REVERT: A 314 GLU cc_start: 0.7452 (pm20) cc_final: 0.7159 (pm20) REVERT: A 327 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6820 (pp20) REVERT: B 19 ARG cc_start: 0.7083 (ttm-80) cc_final: 0.6241 (ttp80) REVERT: B 46 ARG cc_start: 0.7811 (mtp180) cc_final: 0.6411 (mpt180) REVERT: B 118 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7671 (p0) REVERT: B 172 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: B 209 LYS cc_start: 0.7800 (mttm) cc_final: 0.7561 (mttp) REVERT: B 215 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: B 243 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8157 (p) REVERT: B 254 ASP cc_start: 0.8030 (p0) cc_final: 0.7789 (t0) REVERT: B 336 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8402 (mp) REVERT: D 8 CYS cc_start: 0.5105 (m) cc_final: 0.3936 (t) REVERT: D 11 THR cc_start: 0.7266 (m) cc_final: 0.6683 (p) REVERT: D 22 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.4784 (tpp) REVERT: D 43 ARG cc_start: 0.5708 (mtp180) cc_final: 0.4688 (mtt180) REVERT: D 91 ARG cc_start: 0.5716 (mtm-85) cc_final: 0.5345 (mtm110) REVERT: D 92 SER cc_start: 0.6836 (p) cc_final: 0.6287 (p) REVERT: D 173 LYS cc_start: 0.6704 (mtpt) cc_final: 0.6221 (ttpt) REVERT: D 183 CYS cc_start: 0.8275 (m) cc_final: 0.7872 (p) REVERT: D 190 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: D 276 MET cc_start: 0.6370 (mmt) cc_final: 0.5556 (ptp) REVERT: D 307 ARG cc_start: 0.6669 (ttm-80) cc_final: 0.6090 (ttp80) REVERT: N 43 LYS cc_start: 0.7507 (ttmm) cc_final: 0.6947 (mmtt) REVERT: N 65 LYS cc_start: 0.7633 (ttpt) cc_final: 0.6779 (tptm) REVERT: N 89 GLU cc_start: 0.7873 (pp20) cc_final: 0.7421 (pm20) outliers start: 29 outliers final: 19 residues processed: 147 average time/residue: 1.1046 time to fit residues: 173.8647 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 310 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 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 215 GLU 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 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 146 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 102 optimal weight: 0.0010 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.156658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117615 restraints weight = 10568.692| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.70 r_work: 0.3315 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4881 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= 0.106 Angle : 0.479 6.114 11647 Z= 0.249 Chirality : 0.040 0.179 1313 Planarity : 0.003 0.035 1480 Dihedral : 6.701 94.070 1325 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.76 % Allowed : 19.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1046 helix: 3.00 (0.25), residues: 390 sheet: 0.29 (0.34), residues: 208 loop : -0.26 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS D 235 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR N 80 ARG 0.006 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 406) hydrogen bonds : angle 3.95214 ( 1146) covalent geometry : bond 0.00247 ( 8604) covalent geometry : angle 0.47890 (11647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7199.70 seconds wall clock time: 125 minutes 49.71 seconds (7549.71 seconds total)