Starting phenix.real_space_refine on Thu Jul 2 19:13:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8haf_34587/07_2026/8haf_34587.cif Found real_map, /net/cci-nas-00/data/ceres_data/8haf_34587/07_2026/8haf_34587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8haf_34587/07_2026/8haf_34587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8haf_34587/07_2026/8haf_34587.map" model { file = "/net/cci-nas-00/data/ceres_data/8haf_34587/07_2026/8haf_34587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8haf_34587/07_2026/8haf_34587.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8haf_34587/07_2026/8haf_34587.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8haf_34587/07_2026/8haf_34587.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6258 2.51 5 N 1635 2.21 5 O 1730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9681 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "P" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 301 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "R" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3029 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 11, 'TRANS': 357} Chain breaks: 3 Chain: "R" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 366 Unusual residues: {'CLR': 6, 'PLM': 11} Classifications: {'undetermined': 17} Link IDs: {None: 16} Time building chain proxies: 2.17, per 1000 atoms: 0.22 Number of scatterers: 9681 At special positions: 0 Unit cell: (103.824, 130.192, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1730 8.00 N 1635 7.00 C 6258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 418.5 milliseconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 41.8% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 removed outlier: 4.267A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 235 through 241 removed outlier: 4.311A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 241 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.525A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.539A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.544A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) 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: 4.217A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.643A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 32 Processing helix chain 'P' and resid 33 through 36 Processing helix chain 'R' and resid 33 through 51 removed outlier: 3.596A pdb=" N PHE R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 172 removed outlier: 3.758A pdb=" N VAL R 171 " --> pdb=" O TYR R 167 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS R 172 " --> pdb=" O SER R 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 167 through 172' Processing helix chain 'R' and resid 178 through 212 removed outlier: 3.553A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 244 removed outlier: 3.735A pdb=" N ALA R 242 " --> pdb=" O PHE R 238 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU R 244 " --> pdb=" O LYS R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 311 removed outlier: 3.653A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 319 Processing helix chain 'R' and resid 320 through 347 removed outlier: 4.052A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.581A pdb=" N ALA R 347 " --> pdb=" O ARG R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 393 Proline residue: R 366 - end of helix removed outlier: 3.971A pdb=" N ILE R 371 " --> pdb=" O ILE R 367 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL R 372 " --> pdb=" O LEU R 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 414 removed outlier: 3.769A pdb=" N ARG R 404 " --> pdb=" O ARG R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.088A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 480 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.711A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N HIS A 34 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE A 222 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A 36 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG A 35 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE A 245 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 37 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A 247 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A 39 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ASP A 249 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.772A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.684A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.306A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.004A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.423A 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: 6.999A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.632A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.507A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.526A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG N 38 " --> pdb=" O GLU N 46 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1284 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: 1.52 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3073 1.35 - 1.46: 2394 1.46 - 1.58: 4348 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9897 Sorted by residual: bond pdb=" C1 PLM R1507 " pdb=" C2 PLM R1507 " ideal model delta sigma weight residual 1.542 1.573 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 PLM R1501 " pdb=" C2 PLM R1501 " ideal model delta sigma weight residual 1.542 1.572 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 PLM R1511 " pdb=" C2 PLM R1511 " ideal model delta sigma weight residual 1.542 1.571 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 PLM R1504 " pdb=" C2 PLM R1504 " ideal model delta sigma weight residual 1.542 1.571 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 PLM R1503 " pdb=" C2 PLM R1503 " ideal model delta sigma weight residual 1.542 1.571 -0.029 2.00e-02 2.50e+03 2.05e+00 ... (remaining 9892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.48: 13355 6.48 - 12.96: 7 12.96 - 19.44: 5 19.44 - 25.92: 0 25.92 - 32.39: 2 Bond angle restraints: 13369 Sorted by residual: angle pdb=" C17 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sigma weight residual 110.18 77.79 32.39 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C12 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sigma weight residual 111.01 78.96 32.05 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C4 CLR R1512 " pdb=" C3 CLR R1512 " pdb=" O1 CLR R1512 " ideal model delta sigma weight residual 111.96 130.39 -18.43 3.00e+00 1.11e-01 3.77e+01 angle pdb=" C12 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C17 CLR R1515 " ideal model delta sigma weight residual 116.52 133.93 -17.41 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C14 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sigma weight residual 112.24 95.10 17.14 3.00e+00 1.11e-01 3.27e+01 ... (remaining 13364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.32: 5304 20.32 - 40.64: 441 40.64 - 60.95: 93 60.95 - 81.27: 2 81.27 - 101.59: 2 Dihedral angle restraints: 5842 sinusoidal: 2446 harmonic: 3396 Sorted by residual: dihedral pdb=" CB CYS R 131 " pdb=" SG CYS R 131 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 153.39 -60.39 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CA PHE R 311 " pdb=" C PHE R 311 " pdb=" N MET R 312 " pdb=" CA MET R 312 " ideal model delta harmonic sigma weight residual 180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C10 CLR R1516 " pdb=" C1 CLR R1516 " pdb=" C2 CLR R1516 " pdb=" C3 CLR R1516 " ideal model delta sinusoidal sigma weight residual -56.83 44.76 -101.59 1 3.00e+01 1.11e-03 1.28e+01 ... (remaining 5839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 1468 0.349 - 0.699: 1 0.699 - 1.048: 1 1.048 - 1.397: 0 1.397 - 1.746: 1 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C13 CLR R1515 " pdb=" C12 CLR R1515 " pdb=" C14 CLR R1515 " pdb=" C17 CLR R1515 " both_signs ideal model delta sigma weight residual False -2.93 -1.19 -1.75 2.00e-01 2.50e+01 7.62e+01 chirality pdb=" C3 CLR R1512 " pdb=" C2 CLR R1512 " pdb=" C4 CLR R1512 " pdb=" O1 CLR R1512 " both_signs ideal model delta sigma weight residual False -2.46 -1.41 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" C3 CLR R1515 " pdb=" C2 CLR R1515 " pdb=" C4 CLR R1515 " pdb=" O1 CLR R1515 " both_signs ideal model delta sigma weight residual False -2.46 -3.00 0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 1468 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 164 " -0.024 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP R 164 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP R 164 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP R 164 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 164 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 164 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 164 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 164 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 164 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 164 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 137 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C ASP R 137 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP R 137 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE R 138 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 21 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C ARG P 21 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG P 21 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE P 22 " -0.013 2.00e-02 2.50e+03 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 8 2.32 - 2.96: 4397 2.96 - 3.61: 13918 3.61 - 4.25: 21038 4.25 - 4.90: 36186 Nonbonded interactions: 75547 Sorted by model distance: nonbonded pdb=" O1 CLR R1512 " pdb=" O1 CLR R1515 " model vdw 1.671 2.432 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.043 3.040 nonbonded pdb=" O1 CLR R1512 " pdb=" C2 CLR R1515 " model vdw 2.061 2.752 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.170 3.040 nonbonded pdb=" C4 CLR R1512 " pdb=" O1 CLR R1515 " model vdw 2.236 2.752 ... (remaining 75542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.680 Find NCS groups from input model: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.003 0.040 9903 Z= 0.152 Angle : 0.821 32.394 13377 Z= 0.376 Chirality : 0.068 1.746 1471 Planarity : 0.004 0.052 1652 Dihedral : 14.577 101.588 3636 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.40 % Allowed : 17.96 % Favored : 81.64 % 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: 0.83 (0.26), residues: 1147 helix: 2.05 (0.25), residues: 460 sheet: 0.92 (0.42), residues: 175 loop : -1.03 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 43 TYR 0.032 0.001 TYR R 191 PHE 0.017 0.001 PHE R 39 TRP 0.058 0.001 TRP R 164 HIS 0.004 0.001 HIS R 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 9897) covalent geometry : angle 0.82135 / 0.38 (13369) SS BOND : bond 0.00209 / 0.11 ( 4) SS BOND : angle 0.93401 / 0.34 ( 8) hydrogen bonds : bond 0.19147 / 12.44 ( 449) hydrogen bonds : angle 5.88251 / 4.26 ( 1284) Misc. bond : bond 0.01743 / 0.83 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6267 (tmm) cc_final: 0.5877 (tmm) REVERT: A 208 PHE cc_start: 0.8405 (m-80) cc_final: 0.8202 (m-80) REVERT: A 211 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7885 (mttt) REVERT: A 283 ARG cc_start: 0.7363 (ptt180) cc_final: 0.6982 (ptp-170) REVERT: A 342 ARG cc_start: 0.7316 (ttp-170) cc_final: 0.7096 (ttt-90) REVERT: B 188 MET cc_start: 0.7690 (mmm) cc_final: 0.7372 (mmm) REVERT: B 217 MET cc_start: 0.6992 (ppp) cc_final: 0.6234 (ppp) REVERT: B 289 TYR cc_start: 0.7813 (m-80) cc_final: 0.6921 (m-80) REVERT: B 295 ASN cc_start: 0.8242 (m-40) cc_final: 0.8003 (m-40) REVERT: N 34 MET cc_start: 0.8015 (mmm) cc_final: 0.7501 (mmm) REVERT: N 49 SER cc_start: 0.8222 (p) cc_final: 0.7787 (t) REVERT: R 240 LYS cc_start: 0.7317 (tmmt) cc_final: 0.7086 (ttpt) REVERT: R 342 VAL cc_start: 0.7439 (t) cc_final: 0.7113 (p) REVERT: R 404 ARG cc_start: 0.7230 (mtt90) cc_final: 0.7022 (mtt90) REVERT: R 413 LEU cc_start: 0.7112 (tp) cc_final: 0.6834 (tp) outliers start: 4 outliers final: 3 residues processed: 217 average time/residue: 0.1235 time to fit residues: 34.9908 Evaluate side-chains 192 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 135 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN A 271 ASN A 362 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 220 GLN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115044 restraints weight = 13145.245| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.81 r_work: 0.3283 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9903 Z= 0.207 Angle : 0.826 32.227 13377 Z= 0.370 Chirality : 0.072 1.770 1471 Planarity : 0.005 0.044 1652 Dihedral : 8.704 104.325 1497 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.20 % Allowed : 17.27 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.25), residues: 1147 helix: 2.18 (0.25), residues: 452 sheet: 0.68 (0.37), residues: 206 loop : -0.98 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 31 TYR 0.026 0.002 TYR R 191 PHE 0.026 0.002 PHE R 335 TRP 0.017 0.002 TRP B 339 HIS 0.006 0.002 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 ( 9897) covalent geometry : angle 0.82569 / 0.37 (13369) SS BOND : bond 0.00211 / 0.11 ( 4) SS BOND : angle 0.95046 / 0.34 ( 8) hydrogen bonds : bond 0.04584 / 3.17 ( 449) hydrogen bonds : angle 4.04310 / 2.86 ( 1284) Misc. bond : bond 0.01708 / 0.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6656 (tmm) cc_final: 0.6288 (tmm) REVERT: A 314 GLU cc_start: 0.7452 (mp0) cc_final: 0.7189 (mp0) REVERT: A 346 LEU cc_start: 0.7802 (mm) cc_final: 0.7478 (mt) REVERT: B 188 MET cc_start: 0.8176 (mmm) cc_final: 0.7860 (mmm) REVERT: B 217 MET cc_start: 0.7813 (ppp) cc_final: 0.7020 (ppp) REVERT: B 219 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7589 (mtp85) REVERT: B 221 THR cc_start: 0.8015 (m) cc_final: 0.7687 (t) REVERT: B 275 SER cc_start: 0.7907 (t) cc_final: 0.7627 (t) REVERT: B 316 SER cc_start: 0.8352 (t) cc_final: 0.8035 (p) REVERT: B 317 CYS cc_start: 0.7946 (p) cc_final: 0.7655 (p) REVERT: N 60 TYR cc_start: 0.8410 (m-80) cc_final: 0.8181 (m-80) REVERT: N 108 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: R 36 GLU cc_start: 0.7158 (tp30) cc_final: 0.6946 (tp30) REVERT: R 181 ARG cc_start: 0.7127 (mmm-85) cc_final: 0.6771 (mmm-85) REVERT: R 342 VAL cc_start: 0.7901 (t) cc_final: 0.7583 (p) REVERT: R 360 LYS cc_start: 0.8369 (ttpp) cc_final: 0.7777 (ptpp) REVERT: R 408 LYS cc_start: 0.8424 (tmtt) cc_final: 0.8203 (tptp) REVERT: R 443 TYR cc_start: 0.8426 (t80) cc_final: 0.8195 (t80) outliers start: 22 outliers final: 13 residues processed: 215 average time/residue: 0.1135 time to fit residues: 32.4915 Evaluate side-chains 202 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.0570 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115192 restraints weight = 13153.936| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.80 r_work: 0.3281 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9903 Z= 0.163 Angle : 0.764 32.273 13377 Z= 0.334 Chirality : 0.071 1.780 1471 Planarity : 0.004 0.039 1652 Dihedral : 8.311 104.793 1488 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.89 % Allowed : 17.76 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.02 (0.26), residues: 1147 helix: 2.27 (0.25), residues: 456 sheet: 0.71 (0.38), residues: 196 loop : -0.89 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 390 TYR 0.025 0.002 TYR R 191 PHE 0.028 0.002 PHE R 335 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 9897) covalent geometry : angle 0.76369 / 0.33 (13369) SS BOND : bond 0.00191 / 0.10 ( 4) SS BOND : angle 0.69499 / 0.30 ( 8) hydrogen bonds : bond 0.04367 / 2.98 ( 449) hydrogen bonds : angle 3.88228 / 2.75 ( 1284) Misc. bond : bond 0.01706 / 0.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6633 (tmm) cc_final: 0.6317 (tmm) REVERT: A 309 GLU cc_start: 0.7817 (mp0) cc_final: 0.7427 (mp0) REVERT: A 314 GLU cc_start: 0.7516 (mp0) cc_final: 0.7185 (mp0) REVERT: A 346 LEU cc_start: 0.7864 (mm) cc_final: 0.7445 (mt) REVERT: B 188 MET cc_start: 0.8171 (mmm) cc_final: 0.7889 (mmm) REVERT: B 217 MET cc_start: 0.7817 (ppp) cc_final: 0.6968 (ppp) REVERT: B 219 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7556 (mtp85) REVERT: B 245 SER cc_start: 0.8477 (p) cc_final: 0.8256 (m) REVERT: B 275 SER cc_start: 0.7875 (t) cc_final: 0.7616 (t) REVERT: B 289 TYR cc_start: 0.8613 (m-80) cc_final: 0.8290 (m-80) REVERT: B 298 ASP cc_start: 0.7634 (t0) cc_final: 0.7282 (t0) REVERT: B 316 SER cc_start: 0.8361 (t) cc_final: 0.7988 (p) REVERT: B 317 CYS cc_start: 0.7965 (p) cc_final: 0.7713 (p) REVERT: N 108 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: R 36 GLU cc_start: 0.7175 (tp30) cc_final: 0.6960 (tp30) REVERT: R 181 ARG cc_start: 0.7025 (mmm-85) cc_final: 0.6666 (mmm-85) REVERT: R 233 ARG cc_start: 0.8354 (ttt180) cc_final: 0.8068 (ttt180) REVERT: R 321 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7716 (tt) REVERT: R 342 VAL cc_start: 0.7929 (t) cc_final: 0.7592 (p) REVERT: R 360 LYS cc_start: 0.8347 (ttpp) cc_final: 0.7829 (ptpp) outliers start: 29 outliers final: 18 residues processed: 206 average time/residue: 0.1352 time to fit residues: 36.4806 Evaluate side-chains 199 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 HIS N 13 GLN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.139276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114327 restraints weight = 13264.236| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.81 r_work: 0.3266 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9903 Z= 0.157 Angle : 0.759 32.036 13377 Z= 0.329 Chirality : 0.071 1.794 1471 Planarity : 0.004 0.035 1652 Dihedral : 8.223 105.200 1488 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.09 % Allowed : 18.86 % Favored : 78.04 % 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 (0.26), residues: 1147 helix: 2.36 (0.25), residues: 451 sheet: 0.53 (0.37), residues: 196 loop : -0.91 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 383 TYR 0.024 0.002 TYR R 191 PHE 0.023 0.002 PHE R 335 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 9897) covalent geometry : angle 0.75884 / 0.33 (13369) SS BOND : bond 0.00193 / 0.10 ( 4) SS BOND : angle 0.67814 / 0.28 ( 8) hydrogen bonds : bond 0.04102 / 2.83 ( 449) hydrogen bonds : angle 3.81133 / 2.69 ( 1284) Misc. bond : bond 0.01704 / 0.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6674 (tmm) cc_final: 0.6252 (tmm) REVERT: A 25 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8012 (ttmm) REVERT: A 309 GLU cc_start: 0.7817 (mp0) cc_final: 0.7452 (mp0) REVERT: A 314 GLU cc_start: 0.7541 (mp0) cc_final: 0.7158 (mp0) REVERT: A 343 ASP cc_start: 0.7639 (t0) cc_final: 0.7371 (m-30) REVERT: A 344 GLU cc_start: 0.7922 (tp30) cc_final: 0.7410 (tp30) REVERT: A 346 LEU cc_start: 0.7900 (mm) cc_final: 0.7377 (mt) REVERT: B 188 MET cc_start: 0.8128 (mmm) cc_final: 0.7920 (mmm) REVERT: B 217 MET cc_start: 0.7837 (ppp) cc_final: 0.7033 (ppp) REVERT: B 219 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7585 (mtp85) REVERT: B 221 THR cc_start: 0.7994 (m) cc_final: 0.7606 (t) REVERT: B 245 SER cc_start: 0.8471 (p) cc_final: 0.8125 (m) REVERT: B 262 MET cc_start: 0.7493 (pmm) cc_final: 0.7276 (ptp) REVERT: B 275 SER cc_start: 0.7865 (t) cc_final: 0.7597 (t) REVERT: B 289 TYR cc_start: 0.8658 (m-80) cc_final: 0.8402 (m-80) REVERT: B 316 SER cc_start: 0.8329 (t) cc_final: 0.7945 (p) REVERT: B 317 CYS cc_start: 0.7907 (p) cc_final: 0.7611 (p) REVERT: N 108 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: R 36 GLU cc_start: 0.7182 (tp30) cc_final: 0.6978 (tp30) REVERT: R 181 ARG cc_start: 0.7045 (mmm-85) cc_final: 0.6697 (mmm-85) REVERT: R 321 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7668 (tt) REVERT: R 342 VAL cc_start: 0.7954 (t) cc_final: 0.7638 (p) REVERT: R 360 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7960 (pttm) REVERT: R 368 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7825 (mp) outliers start: 31 outliers final: 21 residues processed: 218 average time/residue: 0.1193 time to fit residues: 34.3636 Evaluate side-chains 216 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 13 GLN N 31 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.137114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112058 restraints weight = 13186.542| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.79 r_work: 0.3233 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 9903 Z= 0.238 Angle : 0.797 31.877 13377 Z= 0.354 Chirality : 0.073 1.812 1471 Planarity : 0.004 0.034 1652 Dihedral : 8.291 105.477 1488 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.09 % Allowed : 18.66 % Favored : 77.25 % 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: 0.81 (0.25), residues: 1147 helix: 2.13 (0.25), residues: 451 sheet: 0.48 (0.36), residues: 204 loop : -0.98 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 31 TYR 0.024 0.002 TYR R 191 PHE 0.030 0.002 PHE R 335 TRP 0.014 0.002 TRP B 339 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 ( 9897) covalent geometry : angle 0.79674 / 0.35 (13369) SS BOND : bond 0.00278 / 0.14 ( 4) SS BOND : angle 0.74890 / 0.36 ( 8) hydrogen bonds : bond 0.04715 / 3.23 ( 449) hydrogen bonds : angle 3.97226 / 2.79 ( 1284) Misc. bond : bond 0.01699 / 0.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6704 (tmm) cc_final: 0.6299 (tmm) REVERT: A 300 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8115 (ttmt) REVERT: A 309 GLU cc_start: 0.7837 (mp0) cc_final: 0.7467 (mp0) REVERT: A 314 GLU cc_start: 0.7514 (mp0) cc_final: 0.7143 (mp0) REVERT: A 343 ASP cc_start: 0.7798 (t0) cc_final: 0.7511 (m-30) REVERT: A 344 GLU cc_start: 0.8012 (tp30) cc_final: 0.7533 (tp30) REVERT: B 19 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7473 (ttp80) REVERT: B 171 ILE cc_start: 0.7150 (mm) cc_final: 0.6925 (mm) REVERT: B 217 MET cc_start: 0.7865 (ppp) cc_final: 0.7119 (ppp) REVERT: B 219 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7523 (mtt-85) REVERT: B 221 THR cc_start: 0.8017 (m) cc_final: 0.7629 (t) REVERT: B 245 SER cc_start: 0.8515 (p) cc_final: 0.8177 (m) REVERT: B 262 MET cc_start: 0.7568 (pmm) cc_final: 0.7305 (ptp) REVERT: B 275 SER cc_start: 0.7907 (t) cc_final: 0.7644 (t) REVERT: B 316 SER cc_start: 0.8346 (t) cc_final: 0.7924 (p) REVERT: B 317 CYS cc_start: 0.7838 (p) cc_final: 0.7601 (p) REVERT: N 108 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7782 (m-80) REVERT: R 35 GLU cc_start: 0.7353 (mp0) cc_final: 0.6720 (mp0) REVERT: R 36 GLU cc_start: 0.7282 (tp30) cc_final: 0.7065 (tp30) REVERT: R 181 ARG cc_start: 0.7134 (mmm-85) cc_final: 0.6778 (mmm-85) REVERT: R 321 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7647 (tt) REVERT: R 342 VAL cc_start: 0.8014 (t) cc_final: 0.7682 (p) REVERT: R 360 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8011 (pttm) outliers start: 41 outliers final: 30 residues processed: 220 average time/residue: 0.1241 time to fit residues: 36.0652 Evaluate side-chains 220 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 90 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114481 restraints weight = 13119.278| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.81 r_work: 0.3266 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9903 Z= 0.128 Angle : 0.743 31.742 13377 Z= 0.320 Chirality : 0.071 1.820 1471 Planarity : 0.003 0.033 1652 Dihedral : 8.040 105.406 1488 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.09 % Allowed : 19.86 % Favored : 76.05 % 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 (0.26), residues: 1147 helix: 2.40 (0.25), residues: 451 sheet: 0.48 (0.36), residues: 197 loop : -0.93 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 383 TYR 0.023 0.001 TYR R 191 PHE 0.019 0.001 PHE R 335 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS R 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9897) covalent geometry : angle 0.74295 / 0.32 (13369) SS BOND : bond 0.00155 / 0.08 ( 4) SS BOND : angle 0.60030 / 0.27 ( 8) hydrogen bonds : bond 0.03983 / 2.75 ( 449) hydrogen bonds : angle 3.78713 / 2.65 ( 1284) Misc. bond : bond 0.01694 / 0.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6554 (tmm) cc_final: 0.6178 (tmm) REVERT: A 309 GLU cc_start: 0.7824 (mp0) cc_final: 0.7455 (mp0) REVERT: A 314 GLU cc_start: 0.7540 (mp0) cc_final: 0.7186 (mp0) REVERT: A 343 ASP cc_start: 0.7740 (t0) cc_final: 0.7437 (m-30) REVERT: A 344 GLU cc_start: 0.7903 (tp30) cc_final: 0.7436 (tp30) REVERT: B 200 VAL cc_start: 0.8669 (m) cc_final: 0.8363 (p) REVERT: B 217 MET cc_start: 0.7862 (ppp) cc_final: 0.7130 (ppp) REVERT: B 219 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7500 (mtt-85) REVERT: B 221 THR cc_start: 0.7983 (m) cc_final: 0.7633 (t) REVERT: B 262 MET cc_start: 0.7431 (pmm) cc_final: 0.7218 (ptp) REVERT: B 275 SER cc_start: 0.7902 (t) cc_final: 0.7629 (t) REVERT: B 316 SER cc_start: 0.8320 (t) cc_final: 0.7937 (p) REVERT: B 317 CYS cc_start: 0.7884 (p) cc_final: 0.7614 (p) REVERT: N 13 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: N 108 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: R 35 GLU cc_start: 0.7368 (mp0) cc_final: 0.6610 (mp0) REVERT: R 36 GLU cc_start: 0.7226 (tp30) cc_final: 0.7015 (tp30) REVERT: R 181 ARG cc_start: 0.7016 (mmm-85) cc_final: 0.6668 (mmm-85) REVERT: R 226 LEU cc_start: 0.8102 (tp) cc_final: 0.7782 (tp) REVERT: R 233 ARG cc_start: 0.8338 (ttt180) cc_final: 0.8116 (ttt180) REVERT: R 321 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7622 (tt) REVERT: R 342 VAL cc_start: 0.7993 (t) cc_final: 0.7666 (p) REVERT: R 360 LYS cc_start: 0.8290 (ttpp) cc_final: 0.8010 (pttm) REVERT: R 444 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7470 (mm-30) outliers start: 41 outliers final: 26 residues processed: 222 average time/residue: 0.1107 time to fit residues: 32.9529 Evaluate side-chains 217 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 457 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113778 restraints weight = 13181.908| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.83 r_work: 0.3262 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9903 Z= 0.144 Angle : 0.747 31.602 13377 Z= 0.325 Chirality : 0.072 1.830 1471 Planarity : 0.004 0.039 1652 Dihedral : 7.905 105.586 1488 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.79 % Allowed : 20.76 % Favored : 75.45 % 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: 1.02 (0.26), residues: 1147 helix: 2.42 (0.25), residues: 454 sheet: 0.52 (0.36), residues: 197 loop : -0.97 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 31 TYR 0.024 0.001 TYR R 191 PHE 0.021 0.001 PHE R 335 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9897) covalent geometry : angle 0.74732 / 0.32 (13369) SS BOND : bond 0.00190 / 0.10 ( 4) SS BOND : angle 0.62112 / 0.29 ( 8) hydrogen bonds : bond 0.04007 / 2.76 ( 449) hydrogen bonds : angle 3.73178 / 2.61 ( 1284) Misc. bond : bond 0.01690 / 0.80 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6601 (tmm) cc_final: 0.6232 (tmm) REVERT: A 248 VAL cc_start: 0.8896 (t) cc_final: 0.8668 (p) REVERT: A 309 GLU cc_start: 0.7849 (mp0) cc_final: 0.7499 (mp0) REVERT: A 314 GLU cc_start: 0.7521 (mp0) cc_final: 0.7181 (mp0) REVERT: A 343 ASP cc_start: 0.7702 (t0) cc_final: 0.7399 (m-30) REVERT: A 344 GLU cc_start: 0.7903 (tp30) cc_final: 0.7448 (tp30) REVERT: B 200 VAL cc_start: 0.8715 (m) cc_final: 0.8414 (p) REVERT: B 217 MET cc_start: 0.7845 (ppp) cc_final: 0.7134 (ppp) REVERT: B 221 THR cc_start: 0.7958 (m) cc_final: 0.7573 (t) REVERT: B 275 SER cc_start: 0.7927 (t) cc_final: 0.7654 (t) REVERT: B 316 SER cc_start: 0.8334 (t) cc_final: 0.7909 (p) REVERT: B 317 CYS cc_start: 0.7896 (p) cc_final: 0.7608 (p) REVERT: N 13 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: N 108 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: R 35 GLU cc_start: 0.7382 (mp0) cc_final: 0.6707 (mp0) REVERT: R 181 ARG cc_start: 0.6994 (mmm-85) cc_final: 0.6652 (mmm-85) REVERT: R 195 TYR cc_start: 0.8188 (m-80) cc_final: 0.7861 (m-80) REVERT: R 226 LEU cc_start: 0.8120 (tp) cc_final: 0.7794 (tp) REVERT: R 321 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7636 (tt) REVERT: R 342 VAL cc_start: 0.8045 (t) cc_final: 0.7707 (p) REVERT: R 360 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8019 (pttm) REVERT: R 425 MET cc_start: 0.8447 (ttp) cc_final: 0.8221 (tmm) REVERT: R 444 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7459 (mm-30) outliers start: 38 outliers final: 29 residues processed: 224 average time/residue: 0.1027 time to fit residues: 30.7365 Evaluate side-chains 234 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 341 SER Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 GLN ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.138561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113341 restraints weight = 13070.222| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.79 r_work: 0.3256 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9903 Z= 0.165 Angle : 0.759 31.433 13377 Z= 0.332 Chirality : 0.072 1.842 1471 Planarity : 0.004 0.038 1652 Dihedral : 7.916 105.777 1488 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.19 % Allowed : 20.96 % Favored : 74.85 % 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: 1.05 (0.25), residues: 1147 helix: 2.51 (0.25), residues: 444 sheet: 0.52 (0.36), residues: 204 loop : -0.95 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 31 TYR 0.023 0.001 TYR R 191 PHE 0.024 0.002 PHE R 335 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 9897) covalent geometry : angle 0.75925 / 0.33 (13369) SS BOND : bond 0.00220 / 0.11 ( 4) SS BOND : angle 0.62676 / 0.29 ( 8) hydrogen bonds : bond 0.04178 / 2.88 ( 449) hydrogen bonds : angle 3.78275 / 2.65 ( 1284) Misc. bond : bond 0.01684 / 0.80 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6629 (tmm) cc_final: 0.6258 (tmm) REVERT: A 25 LYS cc_start: 0.8335 (ttmm) cc_final: 0.8118 (ttmm) REVERT: A 248 VAL cc_start: 0.8883 (t) cc_final: 0.8666 (p) REVERT: A 300 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8082 (ttmt) REVERT: A 309 GLU cc_start: 0.7869 (mp0) cc_final: 0.7523 (mp0) REVERT: A 314 GLU cc_start: 0.7516 (mp0) cc_final: 0.7183 (mp0) REVERT: A 343 ASP cc_start: 0.7770 (t0) cc_final: 0.7473 (m-30) REVERT: A 344 GLU cc_start: 0.7901 (tp30) cc_final: 0.7452 (tp30) REVERT: B 200 VAL cc_start: 0.8697 (m) cc_final: 0.8392 (p) REVERT: B 217 MET cc_start: 0.7823 (ppp) cc_final: 0.7138 (ppp) REVERT: B 275 SER cc_start: 0.7941 (t) cc_final: 0.7672 (t) REVERT: B 316 SER cc_start: 0.8359 (t) cc_final: 0.7917 (p) REVERT: B 317 CYS cc_start: 0.7855 (p) cc_final: 0.7565 (p) REVERT: N 13 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: N 108 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: P 13 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7806 (ttmm) REVERT: R 35 GLU cc_start: 0.7345 (mp0) cc_final: 0.6695 (mp0) REVERT: R 181 ARG cc_start: 0.7023 (mmm-85) cc_final: 0.6673 (mmm-85) REVERT: R 195 TYR cc_start: 0.8186 (m-80) cc_final: 0.7861 (m-80) REVERT: R 226 LEU cc_start: 0.8142 (tp) cc_final: 0.7811 (tp) REVERT: R 321 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7638 (tt) REVERT: R 342 VAL cc_start: 0.8065 (t) cc_final: 0.7733 (p) REVERT: R 360 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8012 (pttm) REVERT: R 425 MET cc_start: 0.8463 (ttp) cc_final: 0.8253 (tmm) outliers start: 42 outliers final: 32 residues processed: 230 average time/residue: 0.1103 time to fit residues: 33.6932 Evaluate side-chains 239 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 341 SER Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 358 ASN R 364 GLN R 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115099 restraints weight = 13247.997| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.80 r_work: 0.3301 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9903 Z= 0.115 Angle : 0.736 31.298 13377 Z= 0.317 Chirality : 0.072 1.853 1471 Planarity : 0.003 0.041 1652 Dihedral : 7.715 105.863 1488 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.79 % Allowed : 21.66 % Favored : 74.55 % 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 (0.26), residues: 1147 helix: 2.60 (0.25), residues: 452 sheet: 0.55 (0.36), residues: 201 loop : -0.90 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 31 TYR 0.022 0.001 TYR R 191 PHE 0.020 0.001 PHE R 335 TRP 0.011 0.001 TRP A 234 HIS 0.006 0.001 HIS R 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9897) covalent geometry : angle 0.73594 / 0.32 (13369) SS BOND : bond 0.00155 / 0.08 ( 4) SS BOND : angle 0.55924 / 0.26 ( 8) hydrogen bonds : bond 0.03621 / 2.51 ( 449) hydrogen bonds : angle 3.61711 / 2.54 ( 1284) Misc. bond : bond 0.01682 / 0.80 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6486 (tmm) cc_final: 0.6189 (tmm) REVERT: A 248 VAL cc_start: 0.8867 (t) cc_final: 0.8652 (p) REVERT: A 300 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8036 (ttmt) REVERT: A 309 GLU cc_start: 0.7830 (mp0) cc_final: 0.7502 (mp0) REVERT: A 314 GLU cc_start: 0.7515 (mp0) cc_final: 0.7209 (mp0) REVERT: A 343 ASP cc_start: 0.7652 (t0) cc_final: 0.7348 (m-30) REVERT: A 344 GLU cc_start: 0.7809 (tp30) cc_final: 0.7380 (tp30) REVERT: A 350 THR cc_start: 0.8827 (p) cc_final: 0.8623 (p) REVERT: B 78 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8038 (mtmm) REVERT: B 200 VAL cc_start: 0.8624 (m) cc_final: 0.8379 (p) REVERT: B 217 MET cc_start: 0.7831 (ppp) cc_final: 0.7142 (ppp) REVERT: B 219 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7759 (ttm-80) REVERT: B 275 SER cc_start: 0.7944 (t) cc_final: 0.7660 (t) REVERT: B 316 SER cc_start: 0.8338 (t) cc_final: 0.7915 (p) REVERT: B 317 CYS cc_start: 0.7880 (p) cc_final: 0.7573 (p) REVERT: N 13 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: N 108 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: R 35 GLU cc_start: 0.7326 (mp0) cc_final: 0.6571 (mp0) REVERT: R 181 ARG cc_start: 0.6955 (mmm-85) cc_final: 0.6653 (mmm-85) REVERT: R 195 TYR cc_start: 0.8181 (m-80) cc_final: 0.7932 (m-80) REVERT: R 226 LEU cc_start: 0.8114 (tp) cc_final: 0.7821 (tp) REVERT: R 321 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7629 (tt) REVERT: R 342 VAL cc_start: 0.8044 (t) cc_final: 0.7716 (p) REVERT: R 360 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7997 (pttm) REVERT: R 429 TYR cc_start: 0.8040 (m-10) cc_final: 0.7831 (m-10) outliers start: 38 outliers final: 26 residues processed: 219 average time/residue: 0.1104 time to fit residues: 32.0688 Evaluate side-chains 225 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 341 SER Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 5.9990 chunk 81 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 358 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 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 = 0.138707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113546 restraints weight = 13167.581| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.82 r_work: 0.3269 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9903 Z= 0.158 Angle : 0.757 31.174 13377 Z= 0.331 Chirality : 0.073 1.860 1471 Planarity : 0.004 0.043 1652 Dihedral : 7.749 106.033 1488 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.49 % Allowed : 22.06 % Favored : 74.45 % 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: 1.09 (0.26), residues: 1147 helix: 2.51 (0.25), residues: 452 sheet: 0.52 (0.36), residues: 208 loop : -0.95 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 31 TYR 0.023 0.001 TYR R 191 PHE 0.026 0.002 PHE R 335 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 9897) covalent geometry : angle 0.75759 / 0.33 (13369) SS BOND : bond 0.00213 / 0.11 ( 4) SS BOND : angle 0.58516 / 0.27 ( 8) hydrogen bonds : bond 0.04033 / 2.78 ( 449) hydrogen bonds : angle 3.68676 / 2.58 ( 1284) Misc. bond : bond 0.01678 / 0.80 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6532 (tmm) cc_final: 0.6180 (tmm) REVERT: A 248 VAL cc_start: 0.8876 (t) cc_final: 0.8657 (p) REVERT: A 300 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8074 (ttmt) REVERT: A 309 GLU cc_start: 0.7881 (mp0) cc_final: 0.7555 (mp0) REVERT: A 314 GLU cc_start: 0.7550 (mp0) cc_final: 0.7228 (mp0) REVERT: A 343 ASP cc_start: 0.7692 (t0) cc_final: 0.7393 (m-30) REVERT: A 344 GLU cc_start: 0.7873 (tp30) cc_final: 0.7441 (tp30) REVERT: B 200 VAL cc_start: 0.8647 (m) cc_final: 0.8364 (p) REVERT: B 217 MET cc_start: 0.7822 (ppp) cc_final: 0.7135 (ppp) REVERT: B 275 SER cc_start: 0.7968 (t) cc_final: 0.7695 (t) REVERT: B 316 SER cc_start: 0.8384 (t) cc_final: 0.7907 (p) REVERT: B 317 CYS cc_start: 0.7836 (p) cc_final: 0.7565 (p) REVERT: N 13 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8036 (mp10) REVERT: N 108 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: R 35 GLU cc_start: 0.7402 (mp0) cc_final: 0.6692 (mp0) REVERT: R 181 ARG cc_start: 0.7022 (mmm-85) cc_final: 0.6682 (mmm-85) REVERT: R 226 LEU cc_start: 0.8146 (tp) cc_final: 0.7828 (tp) REVERT: R 321 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7651 (tt) REVERT: R 342 VAL cc_start: 0.8072 (t) cc_final: 0.7744 (p) REVERT: R 360 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.8030 (pttm) outliers start: 35 outliers final: 25 residues processed: 222 average time/residue: 0.1113 time to fit residues: 32.5131 Evaluate side-chains 231 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 341 SER Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.0570 chunk 69 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 358 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.139318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114457 restraints weight = 13222.669| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.78 r_work: 0.3275 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9903 Z= 0.144 Angle : 0.751 31.086 13377 Z= 0.327 Chirality : 0.072 1.865 1471 Planarity : 0.004 0.043 1652 Dihedral : 7.680 106.099 1488 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.59 % Allowed : 21.86 % Favored : 74.55 % 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: 1.11 (0.26), residues: 1147 helix: 2.63 (0.25), residues: 446 sheet: 0.62 (0.36), residues: 203 loop : -1.05 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 31 TYR 0.021 0.001 TYR R 191 PHE 0.025 0.001 PHE R 335 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9897) covalent geometry : angle 0.75081 / 0.33 (13369) SS BOND : bond 0.00189 / 0.10 ( 4) SS BOND : angle 0.56274 / 0.27 ( 8) hydrogen bonds : bond 0.03919 / 2.70 ( 449) hydrogen bonds : angle 3.65919 / 2.56 ( 1284) Misc. bond : bond 0.01674 / 0.80 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.67 seconds wall clock time: 45 minutes 48.66 seconds (2748.66 seconds total)