Starting phenix.real_space_refine on Wed Mar 4 21:14:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kpv_22989/03_2026/7kpv_22989.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kpv_22989/03_2026/7kpv_22989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kpv_22989/03_2026/7kpv_22989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kpv_22989/03_2026/7kpv_22989.map" model { file = "/net/cci-nas-00/data/ceres_data/7kpv_22989/03_2026/7kpv_22989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kpv_22989/03_2026/7kpv_22989.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 77 5.16 5 C 10658 2.51 5 N 2771 2.21 5 O 2943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16449 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2952 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 17, 'TRANS': 339} Chain breaks: 3 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2436 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Chain breaks: 2 Chain: "C" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 4049 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 19, 'TRANS': 467} Chain breaks: 2 Chain: "D" Number of atoms: 7012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 7012 Classifications: {'peptide': 876} Link IDs: {'PTRANS': 51, 'TRANS': 824} Chain breaks: 2 Time building chain proxies: 3.02, per 1000 atoms: 0.18 Number of scatterers: 16449 At special positions: 0 Unit cell: (123.05, 146.59, 155.15, 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 77 16.00 O 2943 8.00 N 2771 7.00 C 10658 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: 1.08 Conformation dependent library (CDL) restraints added in 715.0 milliseconds 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 14 sheets defined 40.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.758A pdb=" N ALA A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.898A pdb=" N GLU A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 259 through 280 removed outlier: 3.733A pdb=" N ASN A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.955A pdb=" N ARG A 331 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.702A pdb=" N LEU A 439 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 34 removed outlier: 4.556A pdb=" N GLN B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 90 Processing helix chain 'B' and resid 92 through 110 removed outlier: 3.728A pdb=" N LEU B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 Processing helix chain 'B' and resid 137 through 149 Processing helix chain 'B' and resid 156 through 171 removed outlier: 4.108A pdb=" N VAL B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 4.032A pdb=" N SER B 183 " --> pdb=" O HIS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 225 through 243 removed outlier: 3.744A pdb=" N ILE B 229 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 285 through 300 Processing helix chain 'B' and resid 304 through 317 removed outlier: 4.236A pdb=" N ILE B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 49 removed outlier: 3.833A pdb=" N ASP C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 97 Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.623A pdb=" N HIS C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 166 through 188 Processing helix chain 'C' and resid 198 through 225 removed outlier: 4.105A pdb=" N MET C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 252 removed outlier: 3.917A pdb=" N ARG C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 272 removed outlier: 3.520A pdb=" N HIS C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 272 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 277 through 288 removed outlier: 3.606A pdb=" N HIS C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.674A pdb=" N CYS C 293 " --> pdb=" O TRP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 333 removed outlier: 3.800A pdb=" N THR C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER C 333 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 372 removed outlier: 3.616A pdb=" N ASN C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 393 Processing helix chain 'C' and resid 399 through 413 Processing helix chain 'C' and resid 1413 through 1417 Processing helix chain 'D' and resid 33 through 37 removed outlier: 4.050A pdb=" N GLN D 36 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 33 through 37' Processing helix chain 'D' and resid 39 through 50 removed outlier: 3.971A pdb=" N PHE D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 125 removed outlier: 3.952A pdb=" N LYS D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 179 through 184 Processing helix chain 'D' and resid 216 through 222 removed outlier: 3.681A pdb=" N THR D 220 " --> pdb=" O GLU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.845A pdb=" N ALA D 300 " --> pdb=" O CYS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 822 removed outlier: 3.658A pdb=" N ARG D 822 " --> pdb=" O PRO D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 859 removed outlier: 4.133A pdb=" N THR D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 893 Processing helix chain 'D' and resid 900 through 904 removed outlier: 3.955A pdb=" N THR D 904 " --> pdb=" O ASN D 900 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 900 through 904' Processing helix chain 'D' and resid 958 through 975 removed outlier: 3.649A pdb=" N CYS D 962 " --> pdb=" O PHE D 958 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER D 964 " --> pdb=" O GLU D 960 " (cutoff:3.500A) Proline residue: D 967 - end of helix Processing helix chain 'D' and resid 1001 through 1019 Processing helix chain 'D' and resid 1042 through 1059 removed outlier: 3.607A pdb=" N ALA D1059 " --> pdb=" O ASN D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1078 Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 3.679A pdb=" N VAL D1089 " --> pdb=" O GLN D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1188 through 1207 removed outlier: 3.876A pdb=" N ASP D1192 " --> pdb=" O ARG D1188 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP D1199 " --> pdb=" O CYS D1195 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1236 removed outlier: 3.587A pdb=" N LEU D1229 " --> pdb=" O PRO D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1265 through 1271 removed outlier: 4.055A pdb=" N ASP D1271 " --> pdb=" O PRO D1267 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1364 removed outlier: 3.622A pdb=" N LEU D1350 " --> pdb=" O ASP D1346 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN D1360 " --> pdb=" O GLU D1356 " (cutoff:3.500A) Processing helix chain 'D' and resid 1365 through 1367 No H-bonds generated for 'chain 'D' and resid 1365 through 1367' Processing helix chain 'D' and resid 1379 through 1392 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 81 removed outlier: 6.803A pdb=" N LYS A 91 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR A 80 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 89 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 88 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 180 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 224 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.596A pdb=" N ILE C 119 " --> pdb=" O ILE C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 1373 through 1377 removed outlier: 6.838A pdb=" N ILE C1366 " --> pdb=" O VAL C1375 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR C1377 " --> pdb=" O TRP C1364 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TRP C1364 " --> pdb=" O THR C1377 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C1365 " --> pdb=" O ARG D1289 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU D1287 " --> pdb=" O TYR C1367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 153 Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 59 removed outlier: 4.626A pdb=" N LEU D 56 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AA8, first strand: chain 'D' and resid 171 through 172 removed outlier: 11.998A pdb=" N HIS D 186 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N LEU D 199 " --> pdb=" O HIS D 186 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D 188 " --> pdb=" O MET D 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 839 through 842 Processing sheet with id=AB1, first strand: chain 'D' and resid 905 through 910 removed outlier: 5.294A pdb=" N SER D1317 " --> pdb=" O PHE D1300 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG D1316 " --> pdb=" O LEU D1339 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D1339 " --> pdb=" O ARG D1316 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D1244 " --> pdb=" O LEU D1340 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N SER D1150 " --> pdb=" O CYS D1214 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE D1216 " --> pdb=" O SER D1150 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D1152 " --> pdb=" O ILE D1216 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR D1218 " --> pdb=" O ILE D1152 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU D1154 " --> pdb=" O THR D1218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 905 through 910 removed outlier: 5.294A pdb=" N SER D1317 " --> pdb=" O PHE D1300 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG D1316 " --> pdb=" O LEU D1339 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D1339 " --> pdb=" O ARG D1316 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D1244 " --> pdb=" O LEU D1340 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE D1213 " --> pdb=" O HIS D1241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 915 through 919 Processing sheet with id=AB4, first strand: chain 'D' and resid 950 through 953 removed outlier: 6.659A pdb=" N LYS D 950 " --> pdb=" O LEU D1030 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE D1032 " --> pdb=" O LYS D 950 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 952 " --> pdb=" O ILE D1032 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE D1029 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYS D1069 " --> pdb=" O ILE D1029 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE D1031 " --> pdb=" O LYS D1069 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE D1071 " --> pdb=" O ILE D1031 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU D1033 " --> pdb=" O ILE D1071 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 1256 through 1257 648 hydrogen bonds defined for protein. 1869 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: 2.85 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4590 1.34 - 1.45: 2939 1.45 - 1.57: 9224 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 16873 Sorted by residual: bond pdb=" CA PRO D1027 " pdb=" C PRO D1027 " ideal model delta sigma weight residual 1.517 1.547 -0.030 9.30e-03 1.16e+04 1.04e+01 bond pdb=" N GLU C 311 " pdb=" CA GLU C 311 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.04e+00 bond pdb=" CA HIS B 63 " pdb=" C HIS B 63 " ideal model delta sigma weight residual 1.528 1.566 -0.038 1.37e-02 5.33e+03 7.73e+00 bond pdb=" N LYS C 310 " pdb=" CA LYS C 310 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.22e-02 6.72e+03 6.61e+00 bond pdb=" N ILE C 343 " pdb=" CA ILE C 343 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.25e-02 6.40e+03 3.93e+00 ... (remaining 16868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 22409 2.65 - 5.31: 395 5.31 - 7.96: 55 7.96 - 10.62: 16 10.62 - 13.27: 2 Bond angle restraints: 22877 Sorted by residual: angle pdb=" N PRO D1027 " pdb=" CA PRO D1027 " pdb=" C PRO D1027 " ideal model delta sigma weight residual 110.70 123.97 -13.27 1.22e+00 6.72e-01 1.18e+02 angle pdb=" C PRO D1027 " pdb=" N PRO D1028 " pdb=" CA PRO D1028 " ideal model delta sigma weight residual 119.76 109.94 9.82 1.03e+00 9.43e-01 9.10e+01 angle pdb=" N HIS B 63 " pdb=" CA HIS B 63 " pdb=" C HIS B 63 " ideal model delta sigma weight residual 110.53 102.80 7.73 1.29e+00 6.01e-01 3.59e+01 angle pdb=" N TYR C 342 " pdb=" CA TYR C 342 " pdb=" C TYR C 342 " ideal model delta sigma weight residual 110.41 116.85 -6.44 1.23e+00 6.61e-01 2.75e+01 angle pdb=" C PRO A 379 " pdb=" N PHE A 380 " pdb=" CA PHE A 380 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 ... (remaining 22872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8809 17.94 - 35.88: 901 35.88 - 53.83: 331 53.83 - 71.77: 90 71.77 - 89.71: 13 Dihedral angle restraints: 10144 sinusoidal: 4172 harmonic: 5972 Sorted by residual: dihedral pdb=" CA LEU D 59 " pdb=" C LEU D 59 " pdb=" N LEU D 60 " pdb=" CA LEU D 60 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ASP D 12 " pdb=" C ASP D 12 " pdb=" N VAL D 13 " pdb=" CA VAL D 13 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA HIS A 196 " pdb=" C HIS A 196 " pdb=" N TYR A 197 " pdb=" CA TYR A 197 " ideal model delta harmonic sigma weight residual 180.00 153.45 26.55 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 10141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2021 0.064 - 0.128: 466 0.128 - 0.192: 50 0.192 - 0.256: 7 0.256 - 0.320: 4 Chirality restraints: 2548 Sorted by residual: chirality pdb=" CA PRO D1027 " pdb=" N PRO D1027 " pdb=" C PRO D1027 " pdb=" CB PRO D1027 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA THR C 11 " pdb=" N THR C 11 " pdb=" C THR C 11 " pdb=" CB THR C 11 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA PHE C 313 " pdb=" N PHE C 313 " pdb=" C PHE C 313 " pdb=" CB PHE C 313 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2545 not shown) Planarity restraints: 2871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 340 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C GLU C 340 " 0.070 2.00e-02 2.50e+03 pdb=" O GLU C 340 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN C 341 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 344 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D1098 " 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO D1099 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D1099 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D1099 " 0.045 5.00e-02 4.00e+02 ... (remaining 2868 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1203 2.73 - 3.28: 15481 3.28 - 3.82: 26243 3.82 - 4.36: 28923 4.36 - 4.90: 50711 Nonbonded interactions: 122561 Sorted by model distance: nonbonded pdb=" N ASP B 65 " pdb=" OD1 ASP B 65 " model vdw 2.193 3.120 nonbonded pdb=" O LEU B 66 " pdb=" ND1 HIS B 67 " model vdw 2.270 3.120 nonbonded pdb=" O ILE B 217 " pdb=" ND2 ASN B 218 " model vdw 2.274 3.120 nonbonded pdb=" OG SER D1159 " pdb=" OD1 ASP D1161 " model vdw 2.287 3.040 nonbonded pdb=" OG SER D1159 " pdb=" O ASP D1161 " model vdw 2.299 3.040 ... (remaining 122556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 0.068 16873 Z= 0.229 Angle : 0.901 13.272 22877 Z= 0.512 Chirality : 0.054 0.320 2548 Planarity : 0.007 0.082 2871 Dihedral : 17.415 89.712 6262 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 17.46 % Allowed : 13.72 % Favored : 68.82 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.15), residues: 1984 helix: -2.35 (0.14), residues: 750 sheet: -2.28 (0.32), residues: 211 loop : -3.56 (0.16), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 19 TYR 0.026 0.002 TYR C 178 PHE 0.023 0.002 PHE D 294 TRP 0.026 0.002 TRP B 14 HIS 0.010 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00468 (16873) covalent geometry : angle 0.90128 (22877) hydrogen bonds : bond 0.14657 ( 625) hydrogen bonds : angle 6.32237 ( 1869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 322 poor density : 378 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.7101 (p0) cc_final: 0.6748 (t0) REVERT: A 182 ILE cc_start: 0.8629 (mt) cc_final: 0.8356 (mt) REVERT: A 198 THR cc_start: 0.5579 (m) cc_final: 0.5136 (p) REVERT: A 230 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7590 (mttt) REVERT: A 256 ARG cc_start: 0.5077 (mtt180) cc_final: 0.3439 (mmm160) REVERT: A 314 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8341 (ptp) REVERT: A 349 TRP cc_start: 0.8089 (t-100) cc_final: 0.7864 (t-100) REVERT: A 398 LYS cc_start: 0.5814 (OUTLIER) cc_final: 0.5526 (tmtt) REVERT: A 408 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.6199 (pm20) REVERT: A 434 LYS cc_start: 0.6944 (mtmm) cc_final: 0.6598 (tptt) REVERT: A 446 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.5243 (p90) REVERT: A 465 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: A 486 ARG cc_start: 0.6968 (tpt90) cc_final: 0.5684 (mtp-110) REVERT: B 24 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 33 CYS cc_start: 0.7472 (t) cc_final: 0.7186 (m) REVERT: B 40 LEU cc_start: 0.7877 (tp) cc_final: 0.7229 (tp) REVERT: B 45 ASP cc_start: 0.3413 (OUTLIER) cc_final: 0.3198 (m-30) REVERT: B 63 HIS cc_start: 0.5962 (OUTLIER) cc_final: 0.5682 (m90) REVERT: B 65 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7137 (p0) REVERT: B 83 MET cc_start: 0.7663 (tpp) cc_final: 0.7281 (ttm) REVERT: B 90 ASN cc_start: 0.5176 (t0) cc_final: 0.4922 (t0) REVERT: B 166 TYR cc_start: 0.8445 (m-80) cc_final: 0.8122 (m-10) REVERT: B 185 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8724 (mtmt) REVERT: C 85 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8013 (mp-120) REVERT: C 95 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: C 159 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6439 (mm-40) REVERT: C 294 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: C 343 ILE cc_start: 0.5461 (OUTLIER) cc_final: 0.5253 (pt) REVERT: C 353 ILE cc_start: 0.8402 (mt) cc_final: 0.7825 (pt) REVERT: C 361 LEU cc_start: 0.8990 (mt) cc_final: 0.8744 (mp) REVERT: C 371 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6513 (tm-30) REVERT: C 1392 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7326 (mtpt) REVERT: C 1423 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7277 (ptt-90) REVERT: D 24 LYS cc_start: 0.8240 (pttp) cc_final: 0.7674 (mttt) REVERT: D 25 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7791 (tttt) REVERT: D 34 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6623 (pttt) REVERT: D 38 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.5320 (m-30) REVERT: D 144 ASN cc_start: 0.8248 (t0) cc_final: 0.8026 (t0) REVERT: D 197 MET cc_start: 0.7582 (ppp) cc_final: 0.7229 (ppp) REVERT: D 296 CYS cc_start: 0.7418 (t) cc_final: 0.6839 (m) REVERT: D 298 GLN cc_start: 0.7621 (tp40) cc_final: 0.6603 (mm-40) REVERT: D 305 ASP cc_start: 0.6267 (OUTLIER) cc_final: 0.5637 (t70) REVERT: D 855 GLU cc_start: 0.7741 (tt0) cc_final: 0.7538 (tt0) REVERT: D 860 ASP cc_start: 0.7937 (t0) cc_final: 0.7563 (t0) REVERT: D 863 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8296 (pt) REVERT: D 916 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8888 (m) REVERT: D 975 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8929 (t0) REVERT: D 1037 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.6947 (p0) REVERT: D 1068 LEU cc_start: 0.8915 (tp) cc_final: 0.8503 (tt) REVERT: D 1162 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8174 (mttm) REVERT: D 1393 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8508 (p) outliers start: 322 outliers final: 106 residues processed: 615 average time/residue: 0.1298 time to fit residues: 119.3020 Evaluate side-chains 351 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 218 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 863 ILE Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 916 VAL Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 959 LYS Chi-restraints excluded: chain D residue 975 ASN Chi-restraints excluded: chain D residue 998 LYS Chi-restraints excluded: chain D residue 1037 ASN Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1057 VAL Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1071 ILE Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1162 LYS Chi-restraints excluded: chain D residue 1181 THR Chi-restraints excluded: chain D residue 1187 SER Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1240 ILE Chi-restraints excluded: chain D residue 1245 VAL Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1279 ASP Chi-restraints excluded: chain D residue 1364 LEU Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1385 VAL Chi-restraints excluded: chain D residue 1393 VAL Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN B 58 ASN B 227 HIS B 269 GLN B 273 ASN B 299 HIS C 17 HIS C1360 ASN D 152 HIS D 167 ASN D 862 ASN D 902 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108403 restraints weight = 33483.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110512 restraints weight = 21647.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111948 restraints weight = 16087.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112913 restraints weight = 13138.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113549 restraints weight = 11415.645| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16873 Z= 0.138 Angle : 0.691 9.024 22877 Z= 0.357 Chirality : 0.045 0.200 2548 Planarity : 0.005 0.068 2871 Dihedral : 11.414 73.845 2426 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 9.76 % Allowed : 19.85 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.17), residues: 1984 helix: -0.48 (0.18), residues: 773 sheet: -1.93 (0.31), residues: 231 loop : -3.23 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D1316 TYR 0.020 0.001 TYR A 319 PHE 0.034 0.002 PHE D 307 TRP 0.018 0.001 TRP C 384 HIS 0.005 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00299 (16873) covalent geometry : angle 0.69083 (22877) hydrogen bonds : bond 0.04195 ( 625) hydrogen bonds : angle 4.66664 ( 1869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 236 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ARG cc_start: 0.5065 (mtt180) cc_final: 0.3385 (mmm160) REVERT: A 314 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8250 (mtm) REVERT: A 357 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: A 408 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.5951 (pp20) REVERT: A 446 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.5597 (p90) REVERT: A 486 ARG cc_start: 0.7008 (tpt90) cc_final: 0.5871 (mtp-110) REVERT: B 24 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7106 (tm-30) REVERT: B 116 ASN cc_start: 0.8290 (t0) cc_final: 0.7936 (t0) REVERT: B 166 TYR cc_start: 0.8615 (m-80) cc_final: 0.8403 (m-10) REVERT: B 185 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8633 (mtmt) REVERT: B 269 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7896 (tp40) REVERT: B 313 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7490 (t70) REVERT: C 85 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8152 (mp-120) REVERT: C 95 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: C 145 LYS cc_start: 0.7969 (mmtm) cc_final: 0.7507 (tppt) REVERT: C 159 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6284 (mp10) REVERT: C 294 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: C 1392 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7340 (mtpt) REVERT: C 1423 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7263 (ptt-90) REVERT: C 1427 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7796 (p90) REVERT: D 24 LYS cc_start: 0.7959 (pttp) cc_final: 0.7741 (mttt) REVERT: D 34 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.5508 (mmmt) REVERT: D 197 MET cc_start: 0.7852 (ppp) cc_final: 0.7057 (ppp) REVERT: D 228 ILE cc_start: 0.8701 (pt) cc_final: 0.8371 (mt) REVERT: D 237 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7768 (mtmm) REVERT: D 296 CYS cc_start: 0.7159 (t) cc_final: 0.6780 (m) REVERT: D 307 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: D 860 ASP cc_start: 0.7566 (t0) cc_final: 0.7133 (t0) REVERT: D 863 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8438 (pt) REVERT: D 916 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.9048 (m) REVERT: D 1223 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8347 (mt) outliers start: 180 outliers final: 95 residues processed: 386 average time/residue: 0.1141 time to fit residues: 69.2516 Evaluate side-chains 299 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 185 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain C residue 1427 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 863 ILE Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 916 VAL Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 958 PHE Chi-restraints excluded: chain D residue 998 LYS Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 69 optimal weight: 8.9990 chunk 171 optimal weight: 0.0870 chunk 93 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN C 270 ASN D 120 ASN D 273 HIS D 298 GLN D 862 ASN D 902 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106570 restraints weight = 34042.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108675 restraints weight = 22226.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110117 restraints weight = 16588.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111090 restraints weight = 13546.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111630 restraints weight = 11816.077| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16873 Z= 0.139 Angle : 0.649 8.963 22877 Z= 0.332 Chirality : 0.045 0.203 2548 Planarity : 0.004 0.058 2871 Dihedral : 9.927 65.258 2320 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 8.24 % Allowed : 21.75 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.18), residues: 1984 helix: 0.19 (0.18), residues: 767 sheet: -1.72 (0.32), residues: 234 loop : -3.01 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 941 TYR 0.018 0.001 TYR A 236 PHE 0.017 0.001 PHE C 392 TRP 0.026 0.001 TRP B 149 HIS 0.005 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00319 (16873) covalent geometry : angle 0.64892 (22877) hydrogen bonds : bond 0.04022 ( 625) hydrogen bonds : angle 4.39035 ( 1869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 196 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.6498 (t0) cc_final: 0.6289 (t0) REVERT: A 256 ARG cc_start: 0.5088 (mtt180) cc_final: 0.3414 (mmm160) REVERT: A 349 TRP cc_start: 0.8165 (t-100) cc_final: 0.7934 (t-100) REVERT: A 359 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8188 (tt) REVERT: A 408 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5770 (pp20) REVERT: A 486 ARG cc_start: 0.7050 (tpt90) cc_final: 0.5863 (mtp-110) REVERT: B 24 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7076 (tm-30) REVERT: B 166 TYR cc_start: 0.8629 (m-80) cc_final: 0.8335 (m-10) REVERT: B 185 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8573 (mtmt) REVERT: B 313 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7570 (t70) REVERT: C 32 ASP cc_start: 0.8179 (t0) cc_final: 0.7755 (t0) REVERT: C 95 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: C 145 LYS cc_start: 0.7893 (mmtm) cc_final: 0.7485 (tppt) REVERT: C 159 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.6280 (mp10) REVERT: C 281 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8826 (t) REVERT: C 294 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: C 1373 LYS cc_start: 0.7389 (pttt) cc_final: 0.7140 (ptmm) REVERT: C 1392 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7298 (mtpt) REVERT: C 1423 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7493 (ptt-90) REVERT: C 1427 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7676 (p90) REVERT: D 24 LYS cc_start: 0.8043 (pttp) cc_final: 0.7754 (mttt) REVERT: D 34 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.5545 (mmmt) REVERT: D 197 MET cc_start: 0.8124 (ppp) cc_final: 0.7322 (ppp) REVERT: D 237 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7985 (mmtt) REVERT: D 307 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7484 (m-10) REVERT: D 916 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8995 (m) REVERT: D 1223 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8409 (mt) outliers start: 152 outliers final: 96 residues processed: 323 average time/residue: 0.1104 time to fit residues: 56.5612 Evaluate side-chains 284 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 173 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain C residue 1427 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 916 VAL Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1181 THR Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1388 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 8 optimal weight: 0.0770 chunk 4 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 66 optimal weight: 0.3980 chunk 149 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN B 182 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN C 85 GLN ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 862 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108120 restraints weight = 34015.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109447 restraints weight = 22867.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110446 restraints weight = 19513.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112049 restraints weight = 15417.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.112063 restraints weight = 13529.832| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 16873 Z= 0.111 Angle : 0.607 8.729 22877 Z= 0.308 Chirality : 0.043 0.214 2548 Planarity : 0.004 0.054 2871 Dihedral : 9.126 60.805 2295 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 7.81 % Allowed : 22.94 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.19), residues: 1984 helix: 0.65 (0.19), residues: 771 sheet: -1.56 (0.32), residues: 234 loop : -2.88 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 485 TYR 0.016 0.001 TYR A 402 PHE 0.021 0.001 PHE D 46 TRP 0.015 0.001 TRP C 264 HIS 0.004 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00247 (16873) covalent geometry : angle 0.60664 (22877) hydrogen bonds : bond 0.03527 ( 625) hydrogen bonds : angle 4.15433 ( 1869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 198 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 256 ARG cc_start: 0.4949 (mtt180) cc_final: 0.3271 (mmm160) REVERT: A 278 HIS cc_start: 0.9015 (OUTLIER) cc_final: 0.8664 (m90) REVERT: A 357 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: A 359 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 408 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.5608 (pp20) REVERT: A 486 ARG cc_start: 0.7066 (tpt90) cc_final: 0.5759 (mtp-110) REVERT: B 24 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 166 TYR cc_start: 0.8537 (m-80) cc_final: 0.8177 (m-10) REVERT: B 185 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8583 (mtmt) REVERT: B 313 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7638 (t70) REVERT: C 32 ASP cc_start: 0.8077 (t0) cc_final: 0.7669 (t0) REVERT: C 145 LYS cc_start: 0.7847 (mmtm) cc_final: 0.7518 (tppt) REVERT: C 159 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6363 (mm-40) REVERT: C 281 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8778 (t) REVERT: C 294 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: C 371 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: C 1392 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7365 (mtpt) REVERT: C 1423 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7462 (ptt-90) REVERT: C 1427 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7755 (p90) REVERT: D 24 LYS cc_start: 0.8116 (pttp) cc_final: 0.7834 (mttt) REVERT: D 34 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.5387 (mmmt) REVERT: D 197 MET cc_start: 0.8137 (ppp) cc_final: 0.7362 (ppp) REVERT: D 237 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7918 (mmpt) REVERT: D 307 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: D 916 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8986 (m) REVERT: D 1066 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8530 (pt) REVERT: D 1223 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8297 (mt) outliers start: 144 outliers final: 95 residues processed: 317 average time/residue: 0.1096 time to fit residues: 55.4784 Evaluate side-chains 292 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 179 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain C residue 1427 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 863 ILE Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 916 VAL Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 998 LYS Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1242 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 74 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106487 restraints weight = 33851.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108572 restraints weight = 21993.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109992 restraints weight = 16442.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110910 restraints weight = 13475.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111587 restraints weight = 11787.830| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16873 Z= 0.123 Angle : 0.611 12.610 22877 Z= 0.309 Chirality : 0.044 0.177 2548 Planarity : 0.004 0.054 2871 Dihedral : 8.812 56.858 2288 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 8.24 % Allowed : 22.99 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.19), residues: 1984 helix: 0.90 (0.19), residues: 771 sheet: -1.42 (0.33), residues: 234 loop : -2.72 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 485 TYR 0.017 0.001 TYR B 79 PHE 0.016 0.001 PHE D 46 TRP 0.035 0.001 TRP A 349 HIS 0.004 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00282 (16873) covalent geometry : angle 0.61126 (22877) hydrogen bonds : bond 0.03514 ( 625) hydrogen bonds : angle 4.08171 ( 1869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 192 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 256 ARG cc_start: 0.4833 (mtt180) cc_final: 0.3286 (mmm160) REVERT: A 278 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8706 (m90) REVERT: A 357 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: A 359 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8241 (tt) REVERT: A 408 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.5836 (pp20) REVERT: A 446 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.5499 (p90) REVERT: A 486 ARG cc_start: 0.7076 (tpt90) cc_final: 0.5947 (mtp-110) REVERT: B 24 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7114 (tm-30) REVERT: B 38 GLN cc_start: 0.7624 (pp30) cc_final: 0.7114 (pp30) REVERT: B 126 TYR cc_start: 0.8831 (t80) cc_final: 0.8445 (t80) REVERT: B 166 TYR cc_start: 0.8545 (m-80) cc_final: 0.8198 (m-10) REVERT: B 185 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8558 (mtmt) REVERT: B 313 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.7677 (t70) REVERT: C 32 ASP cc_start: 0.8132 (t0) cc_final: 0.7712 (t0) REVERT: C 145 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7514 (tppt) REVERT: C 159 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6439 (mm-40) REVERT: C 281 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8797 (t) REVERT: C 294 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: C 1392 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7165 (mtpt) REVERT: C 1427 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7712 (p90) REVERT: D 24 LYS cc_start: 0.8088 (pttp) cc_final: 0.7794 (mttt) REVERT: D 34 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.5594 (mmmt) REVERT: D 197 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7578 (ppp) REVERT: D 237 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7773 (mmpt) REVERT: D 832 ILE cc_start: 0.9115 (pp) cc_final: 0.8789 (pt) REVERT: D 916 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8980 (m) REVERT: D 1223 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8284 (mt) outliers start: 152 outliers final: 107 residues processed: 319 average time/residue: 0.1094 time to fit residues: 55.9537 Evaluate side-chains 296 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 172 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1427 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 916 VAL Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1242 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1298 ILE Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1388 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 41 optimal weight: 0.6980 chunk 134 optimal weight: 0.0040 chunk 2 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 120 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS B 38 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN D 856 GLN D1344 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107617 restraints weight = 33717.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109717 restraints weight = 21975.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111116 restraints weight = 16405.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112083 restraints weight = 13464.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112700 restraints weight = 11741.659| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 16873 Z= 0.106 Angle : 0.601 11.840 22877 Z= 0.300 Chirality : 0.043 0.162 2548 Planarity : 0.004 0.068 2871 Dihedral : 8.481 59.942 2276 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 7.43 % Allowed : 24.30 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1984 helix: 1.18 (0.19), residues: 766 sheet: -1.28 (0.33), residues: 235 loop : -2.61 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 485 TYR 0.018 0.001 TYR B 79 PHE 0.020 0.001 PHE D 46 TRP 0.038 0.001 TRP A 349 HIS 0.008 0.001 HIS A 460 Details of bonding type rmsd covalent geometry : bond 0.00237 (16873) covalent geometry : angle 0.60119 (22877) hydrogen bonds : bond 0.03271 ( 625) hydrogen bonds : angle 3.99169 ( 1869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 198 time to evaluate : 0.567 Fit side-chains REVERT: A 256 ARG cc_start: 0.4798 (mtt180) cc_final: 0.3241 (mmm160) REVERT: A 278 HIS cc_start: 0.9043 (OUTLIER) cc_final: 0.8709 (m90) REVERT: A 340 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8002 (mtm180) REVERT: A 357 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: A 408 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5727 (pp20) REVERT: A 446 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.5594 (p90) REVERT: A 486 ARG cc_start: 0.7148 (tpt90) cc_final: 0.5945 (mtp-110) REVERT: B 24 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7058 (tm-30) REVERT: B 126 TYR cc_start: 0.8698 (t80) cc_final: 0.8212 (t80) REVERT: B 166 TYR cc_start: 0.8507 (m-80) cc_final: 0.8134 (m-10) REVERT: B 185 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8571 (mtmt) REVERT: C 108 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8476 (pp) REVERT: C 145 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7493 (tppt) REVERT: C 159 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6407 (mm-40) REVERT: C 281 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8831 (t) REVERT: C 294 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: C 371 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: C 1387 SER cc_start: 0.8950 (t) cc_final: 0.8640 (p) REVERT: C 1392 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7031 (mtmt) REVERT: C 1423 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7608 (ptt-90) REVERT: D 24 LYS cc_start: 0.8150 (pttp) cc_final: 0.7859 (mttt) REVERT: D 34 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.5540 (mmmt) REVERT: D 197 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7652 (ppp) REVERT: D 237 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7796 (mmpt) REVERT: D 916 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8967 (m) REVERT: D 1233 ARG cc_start: 0.7722 (tpp-160) cc_final: 0.6625 (ttm170) REVERT: D 1293 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7568 (mp10) outliers start: 137 outliers final: 92 residues processed: 311 average time/residue: 0.1128 time to fit residues: 55.8384 Evaluate side-chains 288 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 178 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 1354 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 916 VAL Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 40 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 144 optimal weight: 0.0170 chunk 161 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 145 optimal weight: 0.1980 chunk 120 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN C 228 ASN C 270 ASN C 274 ASN D 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107496 restraints weight = 33662.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.109572 restraints weight = 21797.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110997 restraints weight = 16286.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111952 restraints weight = 13336.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112532 restraints weight = 11610.788| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16873 Z= 0.111 Angle : 0.616 13.149 22877 Z= 0.305 Chirality : 0.043 0.178 2548 Planarity : 0.004 0.052 2871 Dihedral : 8.057 56.754 2263 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 7.38 % Allowed : 25.16 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1984 helix: 1.24 (0.19), residues: 773 sheet: -1.23 (0.34), residues: 228 loop : -2.59 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.024 0.001 TYR A 418 PHE 0.026 0.001 PHE D 46 TRP 0.027 0.001 TRP A 349 HIS 0.003 0.001 HIS C1372 Details of bonding type rmsd covalent geometry : bond 0.00251 (16873) covalent geometry : angle 0.61619 (22877) hydrogen bonds : bond 0.03241 ( 625) hydrogen bonds : angle 3.95455 ( 1869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 185 time to evaluate : 0.461 Fit side-chains REVERT: A 256 ARG cc_start: 0.4780 (mtt180) cc_final: 0.3100 (mmm160) REVERT: A 357 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: A 359 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 408 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.5765 (pp20) REVERT: A 446 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.5610 (p90) REVERT: A 486 ARG cc_start: 0.7163 (tpt90) cc_final: 0.5958 (mtp-110) REVERT: B 24 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7114 (tm-30) REVERT: B 126 TYR cc_start: 0.8654 (t80) cc_final: 0.8345 (t80) REVERT: B 166 TYR cc_start: 0.8509 (m-80) cc_final: 0.8140 (m-10) REVERT: B 185 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8524 (mtpt) REVERT: C 122 THR cc_start: 0.5515 (OUTLIER) cc_final: 0.5153 (p) REVERT: C 145 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7522 (tppt) REVERT: C 159 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6407 (mm-40) REVERT: C 274 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8519 (t0) REVERT: C 281 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8807 (t) REVERT: C 294 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: C 371 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6849 (mm-30) REVERT: C 1392 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7044 (mtmt) REVERT: C 1423 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7598 (ptt-90) REVERT: C 1427 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7633 (p90) REVERT: D 24 LYS cc_start: 0.8126 (pttp) cc_final: 0.7838 (mttt) REVERT: D 34 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.5655 (mtpp) REVERT: D 197 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7687 (ppp) REVERT: D 237 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7840 (mmpt) REVERT: D 916 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.9003 (m) REVERT: D 1233 ARG cc_start: 0.7698 (tpp-160) cc_final: 0.6622 (ttm170) REVERT: D 1293 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7526 (mp10) outliers start: 136 outliers final: 95 residues processed: 298 average time/residue: 0.1072 time to fit residues: 50.7782 Evaluate side-chains 289 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 175 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1354 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain C residue 1427 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 916 VAL Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1242 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 28 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 100 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 66 optimal weight: 0.0170 chunk 2 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** D 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106537 restraints weight = 33790.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108590 restraints weight = 22038.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110018 restraints weight = 16488.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110957 restraints weight = 13517.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111597 restraints weight = 11794.504| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16873 Z= 0.123 Angle : 0.626 13.482 22877 Z= 0.309 Chirality : 0.043 0.172 2548 Planarity : 0.004 0.052 2871 Dihedral : 7.938 56.561 2261 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 7.32 % Allowed : 25.38 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1984 helix: 1.30 (0.19), residues: 772 sheet: -1.19 (0.34), residues: 228 loop : -2.54 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.023 0.001 TYR B 79 PHE 0.032 0.001 PHE C 275 TRP 0.029 0.001 TRP A 349 HIS 0.005 0.001 HIS D 823 Details of bonding type rmsd covalent geometry : bond 0.00285 (16873) covalent geometry : angle 0.62571 (22877) hydrogen bonds : bond 0.03349 ( 625) hydrogen bonds : angle 3.95605 ( 1869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 187 time to evaluate : 0.712 Fit side-chains REVERT: A 256 ARG cc_start: 0.4742 (mtt180) cc_final: 0.3123 (mmm160) REVERT: A 340 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8255 (mtm180) REVERT: A 357 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: A 359 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8218 (tt) REVERT: A 408 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.5829 (pp20) REVERT: A 446 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.5699 (p90) REVERT: A 486 ARG cc_start: 0.7179 (tpt90) cc_final: 0.6015 (mtp-110) REVERT: B 24 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7128 (tm-30) REVERT: B 126 TYR cc_start: 0.8661 (t80) cc_final: 0.8356 (t80) REVERT: B 166 TYR cc_start: 0.8539 (m-80) cc_final: 0.8180 (m-10) REVERT: B 185 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8533 (mtpt) REVERT: B 287 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7608 (mtm) REVERT: C 145 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7558 (tppt) REVERT: C 159 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6423 (mm-40) REVERT: C 218 LYS cc_start: 0.8404 (tppt) cc_final: 0.8184 (tppt) REVERT: C 274 ASN cc_start: 0.8853 (p0) cc_final: 0.8536 (t0) REVERT: C 281 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8777 (t) REVERT: C 371 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6927 (mm-30) REVERT: C 1392 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.7040 (mtmt) REVERT: C 1423 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7556 (ptt-90) REVERT: C 1427 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7607 (p90) REVERT: D 24 LYS cc_start: 0.8132 (pttp) cc_final: 0.7845 (mttt) REVERT: D 34 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.5419 (mtpp) REVERT: D 197 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7724 (ppp) REVERT: D 994 LEU cc_start: 0.8234 (mt) cc_final: 0.8014 (mt) REVERT: D 1061 MET cc_start: 0.7435 (tmm) cc_final: 0.6946 (tpp) REVERT: D 1233 ARG cc_start: 0.7714 (tpp-160) cc_final: 0.6613 (ttm170) REVERT: D 1293 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7523 (mp10) outliers start: 135 outliers final: 100 residues processed: 298 average time/residue: 0.1117 time to fit residues: 52.8904 Evaluate side-chains 295 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 178 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1354 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1376 CYS Chi-restraints excluded: chain C residue 1387 SER Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain C residue 1427 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 856 GLN Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1385 VAL Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 164 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 195 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN D 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.105308 restraints weight = 33808.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106961 restraints weight = 24402.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107584 restraints weight = 18206.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.108141 restraints weight = 16475.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108245 restraints weight = 15580.122| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16873 Z= 0.148 Angle : 0.643 12.815 22877 Z= 0.320 Chirality : 0.044 0.173 2548 Planarity : 0.004 0.052 2871 Dihedral : 7.853 56.407 2255 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 6.94 % Allowed : 25.87 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.19), residues: 1984 helix: 1.35 (0.19), residues: 771 sheet: -1.03 (0.35), residues: 218 loop : -2.54 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 264 TYR 0.022 0.001 TYR A 418 PHE 0.022 0.001 PHE D 46 TRP 0.033 0.001 TRP A 349 HIS 0.004 0.001 HIS D 922 Details of bonding type rmsd covalent geometry : bond 0.00345 (16873) covalent geometry : angle 0.64286 (22877) hydrogen bonds : bond 0.03645 ( 625) hydrogen bonds : angle 3.98252 ( 1869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 181 time to evaluate : 0.722 Fit side-chains REVERT: A 256 ARG cc_start: 0.4824 (mtt180) cc_final: 0.3147 (mmm160) REVERT: A 340 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8242 (mtm180) REVERT: A 357 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: A 359 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7982 (tt) REVERT: A 408 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6064 (pp20) REVERT: A 446 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.5942 (p90) REVERT: A 486 ARG cc_start: 0.7101 (tpt90) cc_final: 0.5932 (mtp-110) REVERT: B 24 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7121 (tm-30) REVERT: B 126 TYR cc_start: 0.8642 (t80) cc_final: 0.8312 (t80) REVERT: B 166 TYR cc_start: 0.8509 (m-80) cc_final: 0.8118 (m-80) REVERT: B 185 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8547 (mtpt) REVERT: B 287 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7635 (mtm) REVERT: C 145 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7654 (tppt) REVERT: C 159 GLN cc_start: 0.6720 (OUTLIER) cc_final: 0.6464 (mm-40) REVERT: C 371 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6955 (mm-30) REVERT: C 1392 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7104 (mtmt) REVERT: C 1423 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7580 (ptt-90) REVERT: C 1427 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7539 (p90) REVERT: D 24 LYS cc_start: 0.8128 (pttp) cc_final: 0.7867 (mttt) REVERT: D 34 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.5190 (mtpp) REVERT: D 197 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.7743 (ppp) REVERT: D 237 LYS cc_start: 0.8413 (mmtt) cc_final: 0.8153 (mmmt) REVERT: D 994 LEU cc_start: 0.8285 (mt) cc_final: 0.8074 (mt) REVERT: D 1061 MET cc_start: 0.7551 (tmm) cc_final: 0.7064 (tpp) REVERT: D 1218 THR cc_start: 0.9451 (p) cc_final: 0.9107 (t) REVERT: D 1233 ARG cc_start: 0.7711 (tpp-160) cc_final: 0.6587 (ttm170) REVERT: D 1293 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: D 1311 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.7115 (m-70) outliers start: 128 outliers final: 93 residues processed: 285 average time/residue: 0.1119 time to fit residues: 50.2221 Evaluate side-chains 283 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 173 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1354 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1376 CYS Chi-restraints excluded: chain C residue 1387 SER Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain C residue 1427 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1291 ILE Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1311 HIS Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1385 VAL Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 182 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 270 ASN C 274 ASN D 235 ASN D 862 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.105192 restraints weight = 33905.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107177 restraints weight = 22313.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108559 restraints weight = 16854.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.109482 restraints weight = 13873.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.110108 restraints weight = 12167.402| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16873 Z= 0.118 Angle : 0.634 12.580 22877 Z= 0.311 Chirality : 0.043 0.181 2548 Planarity : 0.004 0.051 2871 Dihedral : 7.516 56.431 2249 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 6.24 % Allowed : 26.41 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1984 helix: 1.44 (0.19), residues: 773 sheet: -0.95 (0.35), residues: 220 loop : -2.47 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.022 0.001 TYR B 79 PHE 0.040 0.001 PHE D 46 TRP 0.032 0.001 TRP C 264 HIS 0.002 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00273 (16873) covalent geometry : angle 0.63363 (22877) hydrogen bonds : bond 0.03370 ( 625) hydrogen bonds : angle 3.92853 ( 1869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 191 time to evaluate : 0.601 Fit side-chains REVERT: A 256 ARG cc_start: 0.4719 (mtt180) cc_final: 0.3123 (mmm160) REVERT: A 340 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8345 (mtm180) REVERT: A 357 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: A 359 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7891 (tt) REVERT: A 408 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.5986 (pp20) REVERT: A 446 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.5890 (p90) REVERT: A 486 ARG cc_start: 0.7055 (tpt90) cc_final: 0.5896 (mtp-110) REVERT: B 24 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7097 (tm-30) REVERT: B 126 TYR cc_start: 0.8601 (t80) cc_final: 0.8302 (t80) REVERT: B 166 TYR cc_start: 0.8551 (m-80) cc_final: 0.8158 (m-80) REVERT: B 185 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8583 (mtmt) REVERT: B 287 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7575 (mtm) REVERT: C 145 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7567 (tppt) REVERT: C 159 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6445 (mm-40) REVERT: C 274 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8057 (t0) REVERT: C 281 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8754 (t) REVERT: C 286 MET cc_start: 0.8316 (mmp) cc_final: 0.7953 (mmp) REVERT: C 371 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: C 1423 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7620 (ptt-90) REVERT: D 24 LYS cc_start: 0.8095 (pttp) cc_final: 0.7845 (mttt) REVERT: D 34 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.5295 (mtpt) REVERT: D 197 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7747 (ppp) REVERT: D 218 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7768 (tt) REVERT: D 1061 MET cc_start: 0.7508 (tmm) cc_final: 0.7037 (tpp) REVERT: D 1068 LEU cc_start: 0.8441 (tp) cc_final: 0.8241 (tt) REVERT: D 1218 THR cc_start: 0.9487 (p) cc_final: 0.9144 (t) REVERT: D 1233 ARG cc_start: 0.7607 (tpp-160) cc_final: 0.6518 (ttm170) REVERT: D 1261 LEU cc_start: 0.8345 (mm) cc_final: 0.7807 (tp) REVERT: D 1293 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7457 (mp10) outliers start: 115 outliers final: 83 residues processed: 282 average time/residue: 0.1155 time to fit residues: 51.0514 Evaluate side-chains 276 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 176 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1354 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1291 ILE Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1385 VAL Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 129 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 44 optimal weight: 0.4980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105397 restraints weight = 33967.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107049 restraints weight = 23108.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107846 restraints weight = 19126.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108945 restraints weight = 15366.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109043 restraints weight = 14159.323| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 16873 Z= 0.224 Angle : 0.881 59.200 22877 Z= 0.499 Chirality : 0.053 1.399 2548 Planarity : 0.006 0.185 2871 Dihedral : 7.369 56.439 2240 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.69 % Allowed : 26.90 % Favored : 67.41 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.20), residues: 1984 helix: 1.43 (0.19), residues: 773 sheet: -0.95 (0.35), residues: 220 loop : -2.46 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 875 TYR 0.047 0.001 TYR B 79 PHE 0.033 0.001 PHE D 46 TRP 0.028 0.001 TRP C 264 HIS 0.007 0.001 HIS D 273 Details of bonding type rmsd covalent geometry : bond 0.00486 (16873) covalent geometry : angle 0.88071 (22877) hydrogen bonds : bond 0.03459 ( 625) hydrogen bonds : angle 3.94377 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2702.86 seconds wall clock time: 47 minutes 30.09 seconds (2850.09 seconds total)