Starting phenix.real_space_refine on Tue Mar 3 21:03:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvj_32141/03_2026/7vvj_32141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvj_32141/03_2026/7vvj_32141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vvj_32141/03_2026/7vvj_32141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvj_32141/03_2026/7vvj_32141.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvj_32141/03_2026/7vvj_32141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvj_32141/03_2026/7vvj_32141.cif" } resolution = 3.2 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= 0.006 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 51 5.16 5 C 5630 2.51 5 N 1559 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 8872 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1932 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2560 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 424 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 249 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2734 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 11, 'TRANS': 354} Chain breaks: 3 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 1, 'ARG:plan': 10, 'ASP:plan': 4, 'TRP:plan': 4, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 200 Time building chain proxies: 1.80, per 1000 atoms: 0.20 Number of scatterers: 8872 At special positions: 0 Unit cell: (130.725, 104.58, 127.82, 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 51 16.00 O 1632 8.00 N 1559 7.00 C 5630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.09 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 332.7 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 41.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.582A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.927A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.627A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.991A pdb=" N ARG A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.585A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.180A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.603A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.578A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.791A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.371A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.798A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.864A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.793A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 52 Processing helix chain 'R' and resid 182 through 212 removed outlier: 3.637A pdb=" N GLY R 194 " --> pdb=" O ILE R 190 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU R 202 " --> pdb=" O SER R 198 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 219 through 245 Processing helix chain 'R' and resid 277 through 312 removed outlier: 4.406A pdb=" N CYS R 281 " --> pdb=" O GLY R 277 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET R 312 " --> pdb=" O SER R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 329 Processing helix chain 'R' and resid 329 through 346 removed outlier: 3.979A pdb=" N ALA R 333 " --> pdb=" O TRP R 329 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.555A pdb=" N THR R 387 " --> pdb=" O ARG R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 402 through 417 removed outlier: 3.585A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU R 413 " --> pdb=" O SER R 409 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.108A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 480 removed outlier: 3.575A pdb=" N GLU R 469 " --> pdb=" O GLU R 465 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER R 475 " --> pdb=" O LYS R 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 4.007A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.817A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.587A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.213A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.787A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.617A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.876A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.785A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 439 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1449 1.30 - 1.43: 2504 1.43 - 1.57: 5032 1.57 - 1.70: 0 1.70 - 1.84: 74 Bond restraints: 9059 Sorted by residual: bond pdb=" C VAL B 327 " pdb=" O VAL B 327 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.00e-02 1.00e+04 3.79e+01 bond pdb=" C PRO A 351 " pdb=" O PRO A 351 " ideal model delta sigma weight residual 1.233 1.167 0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" C ARG B 137 " pdb=" O ARG B 137 " ideal model delta sigma weight residual 1.234 1.161 0.073 1.22e-02 6.72e+03 3.59e+01 bond pdb=" C ASP N 109 " pdb=" O ASP N 109 " ideal model delta sigma weight residual 1.232 1.170 0.062 1.12e-02 7.97e+03 3.03e+01 bond pdb=" C LEU R 187 " pdb=" O LEU R 187 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.17e-02 7.31e+03 2.75e+01 ... (remaining 9054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 7484 1.53 - 3.07: 3816 3.07 - 4.60: 864 4.60 - 6.14: 104 6.14 - 7.67: 21 Bond angle restraints: 12289 Sorted by residual: angle pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" O CYS N 107 " ideal model delta sigma weight residual 120.36 113.06 7.30 1.08e+00 8.57e-01 4.56e+01 angle pdb=" CA ILE B 80 " pdb=" C ILE B 80 " pdb=" O ILE B 80 " ideal model delta sigma weight residual 120.39 113.60 6.79 1.05e+00 9.07e-01 4.19e+01 angle pdb=" CA GLY N 121 " pdb=" C GLY N 121 " pdb=" O GLY N 121 " ideal model delta sigma weight residual 122.22 118.35 3.87 6.50e-01 2.37e+00 3.55e+01 angle pdb=" CA VAL R 384 " pdb=" C VAL R 384 " pdb=" O VAL R 384 " ideal model delta sigma weight residual 119.29 114.79 4.50 8.40e-01 1.42e+00 2.86e+01 angle pdb=" N VAL R 419 " pdb=" CA VAL R 419 " pdb=" C VAL R 419 " ideal model delta sigma weight residual 111.90 107.69 4.21 8.10e-01 1.52e+00 2.70e+01 ... (remaining 12284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 4796 17.21 - 34.42: 446 34.42 - 51.63: 78 51.63 - 68.84: 22 68.84 - 86.05: 10 Dihedral angle restraints: 5352 sinusoidal: 2002 harmonic: 3350 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -165.05 79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 29.98 63.02 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 150.03 -57.03 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 5349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 863 0.081 - 0.162: 442 0.162 - 0.243: 69 0.243 - 0.325: 8 0.325 - 0.406: 1 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CA LEU A 378 " pdb=" N LEU A 378 " pdb=" C LEU A 378 " pdb=" CB LEU A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA PHE N 108 " pdb=" N PHE N 108 " pdb=" C PHE N 108 " pdb=" CB PHE N 108 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA LEU B 318 " pdb=" N LEU B 318 " pdb=" C LEU B 318 " pdb=" CB LEU B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1380 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 271 " 0.058 2.00e-02 2.50e+03 3.14e-02 2.47e+01 pdb=" CG TRP A 271 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 271 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 271 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 271 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP A 271 " 0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP A 271 " -0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 271 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 271 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 271 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 335 " 0.059 2.00e-02 2.50e+03 3.64e-02 2.31e+01 pdb=" CG PHE B 335 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 335 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE B 335 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE B 335 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE B 335 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE B 335 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.037 2.00e-02 2.50e+03 2.95e-02 1.74e+01 pdb=" CG TYR B 59 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.009 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 618 2.74 - 3.28: 8973 3.28 - 3.82: 13778 3.82 - 4.36: 18956 4.36 - 4.90: 30834 Nonbonded interactions: 73159 Sorted by model distance: nonbonded pdb=" OG1 THR N 28 " pdb=" OD1 ASN N 31 " model vdw 2.205 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.231 3.040 nonbonded pdb=" O MET R 445 " pdb=" OG SER R 449 " model vdw 2.254 3.040 nonbonded pdb=" NE2 HIS B 311 " pdb=" OG1 THR B 329 " model vdw 2.279 3.120 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.291 3.040 ... (remaining 73154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.380 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 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 : 0.015 0.080 9062 Z= 1.080 Angle : 1.784 7.673 12295 Z= 1.297 Chirality : 0.088 0.406 1383 Planarity : 0.009 0.037 1576 Dihedral : 14.241 86.051 3177 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 1.77 % Allowed : 5.53 % Favored : 92.70 % Cbeta Deviations : 0.09 % 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: -1.52 (0.23), residues: 1134 helix: -0.87 (0.23), residues: 427 sheet: -0.90 (0.35), residues: 214 loop : -1.01 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG B 283 TYR 0.058 0.011 TYR B 59 PHE 0.059 0.010 PHE B 335 TRP 0.058 0.013 TRP A 271 HIS 0.019 0.006 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.01507 ( 9059) covalent geometry : angle 1.78291 (12289) SS BOND : bond 0.03350 ( 3) SS BOND : angle 2.88827 ( 6) hydrogen bonds : bond 0.23662 ( 439) hydrogen bonds : angle 8.56813 ( 1257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.307 Fit side-chains REVERT: A 50 ASN cc_start: 0.6210 (m110) cc_final: 0.6007 (p0) REVERT: A 221 MET cc_start: 0.8719 (ttp) cc_final: 0.8488 (ttp) REVERT: A 295 LYS cc_start: 0.7681 (mmpt) cc_final: 0.7309 (mmtp) REVERT: A 376 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7745 (tmm) REVERT: B 161 SER cc_start: 0.9017 (m) cc_final: 0.8772 (m) REVERT: B 175 GLN cc_start: 0.7910 (pm20) cc_final: 0.7364 (pm20) REVERT: B 189 SER cc_start: 0.8980 (m) cc_final: 0.8658 (p) REVERT: N 53 GLN cc_start: 0.8005 (mp10) cc_final: 0.7740 (mp10) REVERT: R 218 THR cc_start: 0.8349 (t) cc_final: 0.8128 (t) REVERT: R 219 ARG cc_start: 0.7075 (ptt90) cc_final: 0.6591 (ptp90) REVERT: R 441 MET cc_start: 0.8456 (mmt) cc_final: 0.7986 (mmt) REVERT: R 443 TYR cc_start: 0.7926 (t80) cc_final: 0.7508 (t80) REVERT: R 445 MET cc_start: 0.8168 (mmm) cc_final: 0.7770 (mmm) REVERT: R 465 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7564 (mt-10) outliers start: 16 outliers final: 6 residues processed: 173 average time/residue: 0.1276 time to fit residues: 28.3507 Evaluate side-chains 132 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 25 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 31 ASN R 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120026 restraints weight = 10702.513| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.70 r_work: 0.3261 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9062 Z= 0.125 Angle : 0.544 7.928 12295 Z= 0.296 Chirality : 0.042 0.149 1383 Planarity : 0.004 0.034 1576 Dihedral : 5.498 58.674 1262 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.88 % Allowed : 11.06 % Favored : 87.06 % 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: 0.08 (0.25), residues: 1134 helix: 1.12 (0.25), residues: 425 sheet: -0.64 (0.33), residues: 224 loop : -0.45 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 396 TYR 0.027 0.002 TYR R 191 PHE 0.016 0.001 PHE R 335 TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9059) covalent geometry : angle 0.54330 (12289) SS BOND : bond 0.00223 ( 3) SS BOND : angle 1.43712 ( 6) hydrogen bonds : bond 0.04605 ( 439) hydrogen bonds : angle 4.93460 ( 1257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.322 Fit side-chains REVERT: A 221 MET cc_start: 0.8783 (ttp) cc_final: 0.8576 (ttp) REVERT: A 333 ASP cc_start: 0.8389 (t70) cc_final: 0.8061 (t0) REVERT: B 175 GLN cc_start: 0.8352 (pm20) cc_final: 0.7744 (pm20) REVERT: B 217 MET cc_start: 0.8154 (ppp) cc_final: 0.7857 (ppp) REVERT: B 262 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8278 (ttm) REVERT: G 21 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6404 (mtt) REVERT: R 39 PHE cc_start: 0.7005 (t80) cc_final: 0.6738 (t80) REVERT: R 186 ARG cc_start: 0.7584 (tmm-80) cc_final: 0.7116 (ttm-80) REVERT: R 228 LEU cc_start: 0.8012 (tp) cc_final: 0.7771 (mt) REVERT: R 296 TYR cc_start: 0.8486 (m-10) cc_final: 0.8179 (m-10) REVERT: R 383 ARG cc_start: 0.6542 (mmp-170) cc_final: 0.6324 (mmp-170) outliers start: 17 outliers final: 9 residues processed: 162 average time/residue: 0.1329 time to fit residues: 27.6536 Evaluate side-chains 149 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 33 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 254 ASN B 32 GLN B 340 ASN N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118290 restraints weight = 10751.964| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.72 r_work: 0.3215 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9062 Z= 0.133 Angle : 0.511 7.410 12295 Z= 0.278 Chirality : 0.042 0.150 1383 Planarity : 0.003 0.036 1576 Dihedral : 4.758 59.629 1253 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.88 % Allowed : 13.16 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.43 (0.25), residues: 1134 helix: 1.53 (0.25), residues: 434 sheet: -0.52 (0.33), residues: 228 loop : -0.38 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 396 TYR 0.013 0.001 TYR R 191 PHE 0.016 0.001 PHE R 335 TRP 0.016 0.002 TRP R 298 HIS 0.004 0.001 HIS P 25 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9059) covalent geometry : angle 0.51108 (12289) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.96046 ( 6) hydrogen bonds : bond 0.04095 ( 439) hydrogen bonds : angle 4.44272 ( 1257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.413 Fit side-chains REVERT: A 24 LYS cc_start: 0.7867 (tptt) cc_final: 0.7413 (tptt) REVERT: A 28 LYS cc_start: 0.8610 (pptt) cc_final: 0.7851 (tptt) REVERT: A 333 ASP cc_start: 0.8344 (t70) cc_final: 0.8089 (t0) REVERT: B 175 GLN cc_start: 0.8420 (pm20) cc_final: 0.7833 (pm20) REVERT: B 217 MET cc_start: 0.8190 (ppp) cc_final: 0.7826 (ppp) REVERT: G 21 MET cc_start: 0.6710 (ttm) cc_final: 0.6257 (mtt) REVERT: N 53 GLN cc_start: 0.8584 (mp10) cc_final: 0.8258 (mp10) REVERT: R 34 LYS cc_start: 0.6903 (tttt) cc_final: 0.6561 (tttp) REVERT: R 35 GLU cc_start: 0.7657 (mp0) cc_final: 0.7434 (mp0) REVERT: R 39 PHE cc_start: 0.6972 (t80) cc_final: 0.6370 (t80) REVERT: R 189 MET cc_start: 0.7572 (tmm) cc_final: 0.7185 (tmm) outliers start: 17 outliers final: 13 residues processed: 154 average time/residue: 0.1329 time to fit residues: 26.3439 Evaluate side-chains 145 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 88 ASN B 340 ASN N 31 ASN R 448 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118840 restraints weight = 10768.485| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.66 r_work: 0.3266 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9062 Z= 0.108 Angle : 0.484 7.411 12295 Z= 0.261 Chirality : 0.041 0.140 1383 Planarity : 0.003 0.036 1576 Dihedral : 4.193 33.317 1251 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.54 % Allowed : 14.27 % Favored : 83.19 % 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: 0.63 (0.25), residues: 1134 helix: 1.77 (0.26), residues: 434 sheet: -0.34 (0.33), residues: 228 loop : -0.40 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 396 TYR 0.027 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS P 25 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9059) covalent geometry : angle 0.48367 (12289) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.95204 ( 6) hydrogen bonds : bond 0.03624 ( 439) hydrogen bonds : angle 4.20260 ( 1257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7836 (tptt) cc_final: 0.7396 (tptt) REVERT: A 28 LYS cc_start: 0.8626 (pptt) cc_final: 0.7857 (tptt) REVERT: A 333 ASP cc_start: 0.8341 (t70) cc_final: 0.8084 (t0) REVERT: B 175 GLN cc_start: 0.8425 (pm20) cc_final: 0.7840 (pm20) REVERT: B 217 MET cc_start: 0.8121 (ppp) cc_final: 0.7761 (ppp) REVERT: G 21 MET cc_start: 0.6715 (ttm) cc_final: 0.6332 (mtt) REVERT: N 53 GLN cc_start: 0.8531 (mp10) cc_final: 0.8088 (mp10) REVERT: R 34 LYS cc_start: 0.6877 (tttt) cc_final: 0.6585 (tttp) REVERT: R 35 GLU cc_start: 0.7707 (mp0) cc_final: 0.7497 (mp0) REVERT: R 39 PHE cc_start: 0.6880 (t80) cc_final: 0.6327 (t80) REVERT: R 431 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6558 (tt0) outliers start: 23 outliers final: 13 residues processed: 153 average time/residue: 0.1170 time to fit residues: 23.5295 Evaluate side-chains 143 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 431 GLU Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 40.0000 chunk 73 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 23 optimal weight: 40.0000 chunk 110 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 220 ASN R 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111954 restraints weight = 10889.983| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.74 r_work: 0.3142 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9062 Z= 0.259 Angle : 0.625 8.600 12295 Z= 0.335 Chirality : 0.046 0.210 1383 Planarity : 0.004 0.042 1576 Dihedral : 4.711 37.632 1250 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.10 % Allowed : 15.04 % Favored : 81.86 % 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: 0.28 (0.25), residues: 1134 helix: 1.26 (0.25), residues: 440 sheet: -0.28 (0.33), residues: 223 loop : -0.52 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 396 TYR 0.028 0.002 TYR R 191 PHE 0.019 0.002 PHE R 335 TRP 0.021 0.002 TRP R 298 HIS 0.006 0.002 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 9059) covalent geometry : angle 0.62009 (12289) SS BOND : bond 0.00565 ( 3) SS BOND : angle 3.68972 ( 6) hydrogen bonds : bond 0.04483 ( 439) hydrogen bonds : angle 4.58127 ( 1257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.314 Fit side-chains REVERT: A 24 LYS cc_start: 0.7985 (tptt) cc_final: 0.7525 (tptt) REVERT: A 28 LYS cc_start: 0.8649 (pptt) cc_final: 0.7855 (tptt) REVERT: B 156 GLN cc_start: 0.8582 (mt0) cc_final: 0.8313 (mt0) REVERT: B 175 GLN cc_start: 0.8549 (pm20) cc_final: 0.7913 (pm20) REVERT: B 217 MET cc_start: 0.8228 (ppp) cc_final: 0.7876 (ppp) REVERT: G 21 MET cc_start: 0.6785 (ttm) cc_final: 0.6451 (mtt) REVERT: N 83 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8365 (mtp) REVERT: R 409 SER cc_start: 0.8453 (p) cc_final: 0.8097 (m) outliers start: 28 outliers final: 24 residues processed: 145 average time/residue: 0.1285 time to fit residues: 24.3042 Evaluate side-chains 147 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 31 ASN R 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116795 restraints weight = 10988.609| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.72 r_work: 0.3213 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9062 Z= 0.158 Angle : 0.560 10.420 12295 Z= 0.300 Chirality : 0.043 0.172 1383 Planarity : 0.003 0.039 1576 Dihedral : 4.817 44.022 1250 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.88 % Allowed : 16.37 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.52 (0.25), residues: 1134 helix: 1.65 (0.25), residues: 428 sheet: -0.19 (0.32), residues: 222 loop : -0.52 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 396 TYR 0.025 0.002 TYR R 191 PHE 0.019 0.001 PHE R 335 TRP 0.016 0.002 TRP R 298 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9059) covalent geometry : angle 0.55250 (12289) SS BOND : bond 0.00786 ( 3) SS BOND : angle 4.29224 ( 6) hydrogen bonds : bond 0.03913 ( 439) hydrogen bonds : angle 4.33083 ( 1257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.343 Fit side-chains REVERT: A 24 LYS cc_start: 0.7944 (tptt) cc_final: 0.7469 (tptt) REVERT: A 28 LYS cc_start: 0.8631 (pptt) cc_final: 0.7812 (tptt) REVERT: A 333 ASP cc_start: 0.8372 (t70) cc_final: 0.8100 (t0) REVERT: B 175 GLN cc_start: 0.8536 (pm20) cc_final: 0.7960 (pm20) REVERT: B 217 MET cc_start: 0.8176 (ppp) cc_final: 0.7790 (ppp) REVERT: B 340 ASN cc_start: 0.7663 (t0) cc_final: 0.7337 (t0) REVERT: G 21 MET cc_start: 0.6734 (ttm) cc_final: 0.6399 (mtt) REVERT: N 6 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7337 (mm-30) REVERT: N 53 GLN cc_start: 0.8590 (mp10) cc_final: 0.8225 (mp10) REVERT: N 83 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8364 (mtp) REVERT: R 35 GLU cc_start: 0.7779 (mp0) cc_final: 0.7527 (mp0) REVERT: R 137 ASP cc_start: 0.5162 (m-30) cc_final: 0.4826 (m-30) REVERT: R 409 SER cc_start: 0.8344 (p) cc_final: 0.7997 (m) REVERT: R 431 GLU cc_start: 0.7044 (tt0) cc_final: 0.6824 (tt0) outliers start: 26 outliers final: 23 residues processed: 144 average time/residue: 0.1257 time to fit residues: 23.7206 Evaluate side-chains 148 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.148351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114627 restraints weight = 11060.598| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.70 r_work: 0.3195 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9062 Z= 0.200 Angle : 0.591 9.880 12295 Z= 0.316 Chirality : 0.044 0.170 1383 Planarity : 0.004 0.041 1576 Dihedral : 4.837 44.954 1250 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.21 % Allowed : 16.70 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.37 (0.25), residues: 1134 helix: 1.55 (0.25), residues: 429 sheet: -0.28 (0.32), residues: 222 loop : -0.62 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 396 TYR 0.026 0.002 TYR R 191 PHE 0.020 0.002 PHE R 335 TRP 0.018 0.002 TRP R 298 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9059) covalent geometry : angle 0.58361 (12289) SS BOND : bond 0.00422 ( 3) SS BOND : angle 4.28059 ( 6) hydrogen bonds : bond 0.04100 ( 439) hydrogen bonds : angle 4.41776 ( 1257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.336 Fit side-chains REVERT: A 24 LYS cc_start: 0.7956 (tptt) cc_final: 0.7475 (tptt) REVERT: A 28 LYS cc_start: 0.8638 (pptt) cc_final: 0.7812 (tptt) REVERT: A 333 ASP cc_start: 0.8441 (t70) cc_final: 0.8191 (t0) REVERT: B 156 GLN cc_start: 0.8534 (mt0) cc_final: 0.8249 (mt0) REVERT: B 175 GLN cc_start: 0.8569 (pm20) cc_final: 0.7953 (pm20) REVERT: B 217 MET cc_start: 0.8214 (ppp) cc_final: 0.7671 (ppp) REVERT: G 47 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.5736 (mp0) REVERT: N 83 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8351 (mtp) REVERT: R 137 ASP cc_start: 0.5061 (m-30) cc_final: 0.4695 (m-30) REVERT: R 409 SER cc_start: 0.8369 (p) cc_final: 0.8031 (m) outliers start: 29 outliers final: 26 residues processed: 144 average time/residue: 0.1336 time to fit residues: 24.7580 Evaluate side-chains 150 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 98 optimal weight: 0.0980 chunk 7 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.152948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119911 restraints weight = 10763.331| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.72 r_work: 0.3277 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9062 Z= 0.098 Angle : 0.493 7.348 12295 Z= 0.265 Chirality : 0.040 0.143 1383 Planarity : 0.003 0.037 1576 Dihedral : 4.368 39.177 1250 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.21 % Allowed : 18.25 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.82 (0.25), residues: 1134 helix: 2.08 (0.26), residues: 425 sheet: -0.22 (0.32), residues: 220 loop : -0.41 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 396 TYR 0.024 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS P 25 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9059) covalent geometry : angle 0.48963 (12289) SS BOND : bond 0.00224 ( 3) SS BOND : angle 2.80937 ( 6) hydrogen bonds : bond 0.03306 ( 439) hydrogen bonds : angle 4.00843 ( 1257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.319 Fit side-chains REVERT: A 15 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6748 (tp30) REVERT: A 24 LYS cc_start: 0.7942 (tptt) cc_final: 0.7465 (tptt) REVERT: A 333 ASP cc_start: 0.8392 (t70) cc_final: 0.8139 (t0) REVERT: B 175 GLN cc_start: 0.8538 (pm20) cc_final: 0.7956 (pm20) REVERT: B 217 MET cc_start: 0.8141 (ppp) cc_final: 0.7728 (ppp) REVERT: G 47 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.5803 (mp0) REVERT: N 53 GLN cc_start: 0.8478 (mp10) cc_final: 0.8190 (mp10) REVERT: R 137 ASP cc_start: 0.5094 (m-30) cc_final: 0.4742 (m-30) REVERT: R 189 MET cc_start: 0.7479 (tmm) cc_final: 0.7252 (tmm) REVERT: R 391 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7166 (pt0) REVERT: R 409 SER cc_start: 0.8166 (p) cc_final: 0.7833 (m) outliers start: 20 outliers final: 13 residues processed: 149 average time/residue: 0.1283 time to fit residues: 24.6850 Evaluate side-chains 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 11 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 358 ASN R 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.121817 restraints weight = 10838.770| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.69 r_work: 0.3280 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9062 Z= 0.102 Angle : 0.503 7.366 12295 Z= 0.268 Chirality : 0.041 0.215 1383 Planarity : 0.003 0.038 1576 Dihedral : 4.259 39.170 1250 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.99 % Allowed : 18.92 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.95 (0.26), residues: 1134 helix: 2.19 (0.25), residues: 431 sheet: -0.22 (0.32), residues: 222 loop : -0.34 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 396 TYR 0.025 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS P 25 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9059) covalent geometry : angle 0.49876 (12289) SS BOND : bond 0.00248 ( 3) SS BOND : angle 2.86106 ( 6) hydrogen bonds : bond 0.03281 ( 439) hydrogen bonds : angle 3.90954 ( 1257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.353 Fit side-chains REVERT: A 15 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6727 (tp30) REVERT: A 24 LYS cc_start: 0.7895 (tptt) cc_final: 0.7425 (tptt) REVERT: A 333 ASP cc_start: 0.8321 (t70) cc_final: 0.8063 (t0) REVERT: B 175 GLN cc_start: 0.8509 (pm20) cc_final: 0.7932 (pm20) REVERT: G 47 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6514 (mt-10) REVERT: R 137 ASP cc_start: 0.5180 (m-30) cc_final: 0.4856 (m-30) REVERT: R 391 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7267 (pt0) REVERT: R 409 SER cc_start: 0.8086 (p) cc_final: 0.7786 (m) outliers start: 18 outliers final: 16 residues processed: 147 average time/residue: 0.1245 time to fit residues: 23.7306 Evaluate side-chains 144 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 79 optimal weight: 0.0870 chunk 15 optimal weight: 0.0030 chunk 76 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 358 ASN R 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.154894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122091 restraints weight = 10795.277| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.73 r_work: 0.3305 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9062 Z= 0.100 Angle : 0.506 7.344 12295 Z= 0.268 Chirality : 0.040 0.177 1383 Planarity : 0.003 0.037 1576 Dihedral : 4.157 37.716 1250 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.88 % Allowed : 18.69 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.98 (0.25), residues: 1134 helix: 2.26 (0.25), residues: 431 sheet: -0.22 (0.32), residues: 221 loop : -0.36 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 396 TYR 0.025 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.019 0.002 TRP B 339 HIS 0.003 0.001 HIS P 25 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9059) covalent geometry : angle 0.50238 (12289) SS BOND : bond 0.00237 ( 3) SS BOND : angle 2.68174 ( 6) hydrogen bonds : bond 0.03166 ( 439) hydrogen bonds : angle 3.84727 ( 1257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.286 Fit side-chains REVERT: A 24 LYS cc_start: 0.7925 (tptt) cc_final: 0.7458 (tptt) REVERT: A 28 LYS cc_start: 0.8684 (pptt) cc_final: 0.8242 (tttt) REVERT: A 333 ASP cc_start: 0.8368 (t70) cc_final: 0.8110 (t0) REVERT: B 175 GLN cc_start: 0.8487 (pm20) cc_final: 0.7922 (pm20) REVERT: B 217 MET cc_start: 0.8107 (ptt) cc_final: 0.7811 (ppp) REVERT: G 47 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6535 (mt-10) REVERT: N 5 GLN cc_start: 0.8388 (mt0) cc_final: 0.7788 (mt0) REVERT: R 137 ASP cc_start: 0.5151 (m-30) cc_final: 0.4849 (m-30) REVERT: R 321 LEU cc_start: 0.7610 (tp) cc_final: 0.7342 (tt) REVERT: R 409 SER cc_start: 0.8050 (p) cc_final: 0.7768 (m) outliers start: 17 outliers final: 16 residues processed: 143 average time/residue: 0.1164 time to fit residues: 21.8977 Evaluate side-chains 143 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 462 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118527 restraints weight = 10850.677| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.69 r_work: 0.3229 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9062 Z= 0.149 Angle : 0.552 8.484 12295 Z= 0.292 Chirality : 0.042 0.155 1383 Planarity : 0.003 0.057 1576 Dihedral : 4.381 41.298 1250 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.88 % Allowed : 19.14 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: 0.88 (0.25), residues: 1134 helix: 2.14 (0.25), residues: 431 sheet: -0.23 (0.32), residues: 220 loop : -0.39 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 396 TYR 0.027 0.002 TYR R 191 PHE 0.018 0.001 PHE R 335 TRP 0.015 0.002 TRP R 298 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9059) covalent geometry : angle 0.54701 (12289) SS BOND : bond 0.00297 ( 3) SS BOND : angle 3.26434 ( 6) hydrogen bonds : bond 0.03506 ( 439) hydrogen bonds : angle 4.03574 ( 1257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2662.01 seconds wall clock time: 46 minutes 8.05 seconds (2768.05 seconds total)