Starting phenix.real_space_refine on Thu Jul 2 14:26:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vab_31836/07_2026/7vab_31836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vab_31836/07_2026/7vab_31836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vab_31836/07_2026/7vab_31836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vab_31836/07_2026/7vab_31836.map" model { file = "/net/cci-nas-00/data/ceres_data/7vab_31836/07_2026/7vab_31836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vab_31836/07_2026/7vab_31836.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vab_31836/07_2026/7vab_31836.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vab_31836/07_2026/7vab_31836.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.096 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 48 5.16 5 C 5616 2.51 5 N 1525 2.21 5 O 1583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 8772 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2399 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 4 Chain: "P" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 220 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 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: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.74, per 1000 atoms: 0.20 Number of scatterers: 8772 At special positions: 0 Unit cell: (81.396, 101.745, 160.65, 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 48 16.00 O 1583 8.00 N 1525 7.00 C 5616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 320.0 milliseconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.4% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'R' and resid 31 through 48 Processing helix chain 'R' and resid 128 through 162 removed outlier: 3.806A pdb=" N ALA R 150 " --> pdb=" O SER R 146 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE R 162 " --> pdb=" O ILE R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 166 removed outlier: 3.526A pdb=" N HIS R 166 " --> pdb=" O ARG R 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 163 through 166' Processing helix chain 'R' and resid 167 through 193 removed outlier: 3.549A pdb=" N ILE R 172 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG R 192 " --> pdb=" O LEU R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 246 removed outlier: 3.739A pdb=" N ILE R 221 " --> pdb=" O ARG R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 281 removed outlier: 3.890A pdb=" N TYR R 259 " --> pdb=" O HIS R 255 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) Proline residue: R 267 - end of helix Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 296 through 328 Proline residue: R 302 - end of helix removed outlier: 4.271A pdb=" N THR R 306 " --> pdb=" O PRO R 302 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR R 327 " --> pdb=" O SER R 323 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 351 removed outlier: 3.959A pdb=" N LEU R 339 " --> pdb=" O TYR R 335 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 368 through 383 removed outlier: 3.621A pdb=" N ALA R 372 " --> pdb=" O ALA R 368 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU R 380 " --> pdb=" O PHE R 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE R 383 " --> pdb=" O PHE R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 394 Processing helix chain 'R' and resid 396 through 411 removed outlier: 3.581A pdb=" N GLY R 406 " --> pdb=" O GLU R 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.956A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.508A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 removed outlier: 3.605A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 218 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.502A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.445A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.646A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.786A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.755A pdb=" N PHE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.753A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.717A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.813A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.756A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.037A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.868A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.922A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.757A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.563A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.583A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.586A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.591A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.556A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.272A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1242 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: 0.83 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2839 1.34 - 1.46: 2008 1.46 - 1.58: 4052 1.58 - 1.70: 0 1.70 - 1.81: 66 Bond restraints: 8965 Sorted by residual: bond pdb=" C5 CLR R 603 " pdb=" C6 CLR R 603 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C5 CLR R 605 " pdb=" C6 CLR R 605 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C5 CLR R 602 " pdb=" C6 CLR R 602 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C5 CLR R 601 " pdb=" C6 CLR R 601 " ideal model delta sigma weight residual 1.332 1.302 0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C ALA R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.30e+00 ... (remaining 8960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 12040 3.11 - 6.22: 115 6.22 - 9.33: 13 9.33 - 12.44: 1 12.44 - 15.55: 1 Bond angle restraints: 12170 Sorted by residual: angle pdb=" C ASP A 229 " pdb=" N TYR A 230 " pdb=" CA TYR A 230 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" CA TYR R 141 " pdb=" CB TYR R 141 " pdb=" CG TYR R 141 " ideal model delta sigma weight residual 113.90 119.75 -5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.40 126.93 -4.53 1.45e+00 4.76e-01 9.77e+00 angle pdb=" C MET R 140 " pdb=" N TYR R 141 " pdb=" CA TYR R 141 " ideal model delta sigma weight residual 121.14 116.04 5.10 1.75e+00 3.27e-01 8.49e+00 angle pdb=" CA LYS B 127 " pdb=" CB LYS B 127 " pdb=" CG LYS B 127 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.05e+00 ... (remaining 12165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 5069 14.99 - 29.98: 153 29.98 - 44.98: 45 44.98 - 59.97: 2 59.97 - 74.96: 6 Dihedral angle restraints: 5275 sinusoidal: 2148 harmonic: 3127 Sorted by residual: dihedral pdb=" CB CYS R 216 " pdb=" SG CYS R 216 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 142.34 -49.34 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -117.55 31.55 1 1.00e+01 1.00e-02 1.42e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1223 0.085 - 0.169: 123 0.169 - 0.254: 11 0.254 - 0.338: 6 0.338 - 0.423: 6 Chirality restraints: 1369 Sorted by residual: chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C14 CLR R 604 " pdb=" C13 CLR R 604 " pdb=" C15 CLR R 604 " pdb=" C8 CLR R 604 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1366 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 298 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 299 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 309 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C ILE R 309 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE R 309 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN R 310 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO N 88 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.025 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2016 2.80 - 3.32: 7579 3.32 - 3.85: 13849 3.85 - 4.37: 15977 4.37 - 4.90: 28255 Nonbonded interactions: 67676 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.270 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.307 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.313 3.040 nonbonded pdb=" NH1 ARG A 209 " pdb=" OD2 ASP N 109 " model vdw 2.360 3.120 ... (remaining 67671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 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 : 0.004 0.052 8968 Z= 0.189 Angle : 0.801 15.553 12176 Z= 0.416 Chirality : 0.062 0.423 1369 Planarity : 0.006 0.049 1514 Dihedral : 8.781 74.961 3246 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.21), residues: 1050 helix: -1.67 (0.18), residues: 409 sheet: -0.85 (0.33), residues: 224 loop : -1.80 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 150 TYR 0.022 0.002 TYR B 264 PHE 0.021 0.002 PHE B 199 TRP 0.024 0.002 TRP A 248 HIS 0.004 0.001 HIS R 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.19 ( 8965) covalent geometry : angle 0.80018 / 0.42 (12170) SS BOND : bond 0.00190 / 0.10 ( 3) SS BOND : angle 1.98691 / 1.52 ( 6) hydrogen bonds : bond 0.14833 / 9.63 ( 425) hydrogen bonds : angle 6.60614 / 4.74 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 137 LEU cc_start: 0.8137 (mt) cc_final: 0.7863 (mt) REVERT: R 181 MET cc_start: 0.7377 (ttm) cc_final: 0.7058 (mtt) REVERT: R 192 ARG cc_start: 0.7505 (mmt-90) cc_final: 0.6621 (mmp-170) REVERT: R 193 LEU cc_start: 0.7915 (mt) cc_final: 0.7612 (tt) REVERT: R 194 LEU cc_start: 0.6093 (tp) cc_final: 0.5861 (tp) REVERT: R 217 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7108 (ttm110) REVERT: R 252 GLU cc_start: 0.4957 (mp0) cc_final: 0.4501 (pt0) REVERT: R 253 GLU cc_start: 0.4556 (pm20) cc_final: 0.3976 (mm-30) REVERT: R 327 THR cc_start: 0.6131 (m) cc_final: 0.5836 (p) REVERT: R 402 GLU cc_start: 0.7518 (tp30) cc_final: 0.7311 (tp30) REVERT: A 15 ARG cc_start: 0.6827 (ttt180) cc_final: 0.6540 (ttt-90) REVERT: A 274 LYS cc_start: 0.7880 (ptmt) cc_final: 0.7597 (ptpp) REVERT: A 310 ASP cc_start: 0.7029 (t70) cc_final: 0.6614 (t0) REVERT: A 311 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7251 (mm-30) REVERT: B 44 GLN cc_start: 0.7858 (mt0) cc_final: 0.7558 (mm-40) REVERT: B 135 VAL cc_start: 0.8096 (t) cc_final: 0.7831 (t) REVERT: B 156 GLN cc_start: 0.7924 (mt0) cc_final: 0.7717 (mt0) REVERT: B 217 MET cc_start: 0.7127 (mtm) cc_final: 0.6457 (mmt) REVERT: B 262 MET cc_start: 0.6875 (ttm) cc_final: 0.6607 (tpt) REVERT: B 280 LYS cc_start: 0.9014 (tttp) cc_final: 0.8766 (ttmm) REVERT: G 21 MET cc_start: 0.8139 (mmt) cc_final: 0.7897 (ttt) REVERT: N 21 SER cc_start: 0.8550 (m) cc_final: 0.8324 (t) REVERT: N 28 THR cc_start: 0.8087 (m) cc_final: 0.7707 (p) REVERT: N 87 LYS cc_start: 0.8101 (mttt) cc_final: 0.7617 (ttmt) REVERT: N 90 ASP cc_start: 0.8245 (t0) cc_final: 0.7939 (m-30) REVERT: N 117 TYR cc_start: 0.8124 (m-10) cc_final: 0.7382 (m-80) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1051 time to fit residues: 36.4508 Evaluate side-chains 170 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 173 HIS R 224 GLN R 230 ASN R 408 HIS A 197 HIS A 204 GLN A 324 HIS A 329 HIS B 62 HIS B 88 ASN B 91 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 31 ASN N 35 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.212618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163981 restraints weight = 8969.631| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.55 r_work: 0.3471 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8968 Z= 0.160 Angle : 0.566 15.075 12176 Z= 0.289 Chirality : 0.041 0.149 1369 Planarity : 0.004 0.051 1514 Dihedral : 4.455 24.265 1246 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.19 % Allowed : 8.77 % Favored : 90.04 % 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: -0.41 (0.24), residues: 1050 helix: 0.92 (0.24), residues: 432 sheet: -0.52 (0.34), residues: 224 loop : -1.41 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 219 TYR 0.027 0.002 TYR R 141 PHE 0.031 0.002 PHE R 376 TRP 0.013 0.002 TRP B 332 HIS 0.008 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 8965) covalent geometry : angle 0.56549 / 0.29 (12170) SS BOND : bond 0.00448 / 0.24 ( 3) SS BOND : angle 0.98264 / 0.58 ( 6) hydrogen bonds : bond 0.03982 / 2.64 ( 425) hydrogen bonds : angle 4.44483 / 3.16 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8012 (mm-30) REVERT: R 174 ILE cc_start: 0.7518 (mt) cc_final: 0.7153 (mm) REVERT: R 181 MET cc_start: 0.8207 (ttm) cc_final: 0.7891 (mtt) REVERT: R 192 ARG cc_start: 0.7232 (mmt-90) cc_final: 0.6505 (mmp-170) REVERT: R 193 LEU cc_start: 0.7679 (mt) cc_final: 0.7340 (tt) REVERT: R 252 GLU cc_start: 0.5201 (mp0) cc_final: 0.4605 (pt0) REVERT: R 253 GLU cc_start: 0.4831 (pm20) cc_final: 0.4314 (mm-30) REVERT: R 289 ARG cc_start: 0.7960 (mtp180) cc_final: 0.7318 (mtm180) REVERT: R 336 ARG cc_start: 0.6102 (mtt180) cc_final: 0.5353 (tpt170) REVERT: R 345 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7213 (t80) REVERT: A 31 ARG cc_start: 0.8219 (mtm110) cc_final: 0.7878 (mtt-85) REVERT: A 259 ASN cc_start: 0.8639 (t0) cc_final: 0.8406 (t0) REVERT: A 274 LYS cc_start: 0.8173 (ptmt) cc_final: 0.7937 (ptpp) REVERT: A 310 ASP cc_start: 0.8018 (t70) cc_final: 0.7711 (t0) REVERT: A 323 ARG cc_start: 0.7484 (mtm-85) cc_final: 0.7183 (mmm160) REVERT: B 10 GLU cc_start: 0.8548 (tt0) cc_final: 0.8344 (tp30) REVERT: B 44 GLN cc_start: 0.8241 (mt0) cc_final: 0.7946 (mm-40) REVERT: B 217 MET cc_start: 0.8019 (mtm) cc_final: 0.7259 (mmt) REVERT: B 264 TYR cc_start: 0.9122 (m-10) cc_final: 0.8915 (m-80) REVERT: N 87 LYS cc_start: 0.7990 (mttt) cc_final: 0.7647 (ttmt) REVERT: N 90 ASP cc_start: 0.8528 (t0) cc_final: 0.8257 (t0) outliers start: 11 outliers final: 6 residues processed: 197 average time/residue: 0.1019 time to fit residues: 26.2734 Evaluate side-chains 166 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 39 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 0.0050 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 242 HIS B 239 ASN B 259 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.209924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.164578 restraints weight = 8868.427| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.93 r_work: 0.3407 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8968 Z= 0.171 Angle : 0.548 12.488 12176 Z= 0.279 Chirality : 0.041 0.139 1369 Planarity : 0.004 0.043 1514 Dihedral : 4.364 26.761 1246 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.49 % Allowed : 10.82 % Favored : 86.69 % 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: 0.16 (0.26), residues: 1050 helix: 1.62 (0.25), residues: 433 sheet: -0.52 (0.33), residues: 230 loop : -1.20 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.022 0.002 TYR R 392 PHE 0.021 0.002 PHE R 386 TRP 0.014 0.001 TRP N 47 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 8965) covalent geometry : angle 0.54833 / 0.28 (12170) SS BOND : bond 0.00171 / 0.09 ( 3) SS BOND : angle 0.75736 / 0.43 ( 6) hydrogen bonds : bond 0.03748 / 2.47 ( 425) hydrogen bonds : angle 4.23780 / 3.04 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7895 (mm-30) REVERT: R 181 MET cc_start: 0.8277 (ttm) cc_final: 0.7873 (mtp) REVERT: R 192 ARG cc_start: 0.7413 (mmt-90) cc_final: 0.6595 (mmp-170) REVERT: R 193 LEU cc_start: 0.7731 (mt) cc_final: 0.7467 (tt) REVERT: R 289 ARG cc_start: 0.7737 (mtp180) cc_final: 0.7280 (mtm180) REVERT: R 336 ARG cc_start: 0.6025 (mtt180) cc_final: 0.5318 (tpt170) REVERT: R 345 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7531 (t80) REVERT: A 15 ARG cc_start: 0.7281 (ttt90) cc_final: 0.6870 (ttt-90) REVERT: A 47 SER cc_start: 0.8537 (m) cc_final: 0.8209 (p) REVERT: A 182 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8073 (p) REVERT: A 193 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7946 (mtmm) REVERT: A 310 ASP cc_start: 0.8076 (t70) cc_final: 0.7820 (t0) REVERT: A 323 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.7180 (mtm110) REVERT: B 262 MET cc_start: 0.7430 (tpt) cc_final: 0.7119 (tpt) REVERT: B 264 TYR cc_start: 0.9173 (m-10) cc_final: 0.8930 (m-80) REVERT: N 87 LYS cc_start: 0.7975 (mttt) cc_final: 0.7713 (ttmt) REVERT: N 90 ASP cc_start: 0.8488 (t0) cc_final: 0.8250 (t0) outliers start: 23 outliers final: 14 residues processed: 173 average time/residue: 0.1113 time to fit residues: 24.9033 Evaluate side-chains 158 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 97 optimal weight: 0.0170 chunk 43 optimal weight: 0.6980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.210809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.162958 restraints weight = 8973.717| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 3.28 r_work: 0.3444 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.123 Angle : 0.495 11.377 12176 Z= 0.253 Chirality : 0.039 0.136 1369 Planarity : 0.003 0.041 1514 Dihedral : 4.128 24.241 1246 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.81 % Allowed : 11.15 % Favored : 86.04 % 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: 0.54 (0.26), residues: 1050 helix: 2.04 (0.25), residues: 433 sheet: -0.36 (0.33), residues: 228 loop : -1.11 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 314 TYR 0.017 0.001 TYR R 392 PHE 0.016 0.001 PHE R 386 TRP 0.012 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8965) covalent geometry : angle 0.49517 / 0.25 (12170) SS BOND : bond 0.00201 / 0.10 ( 3) SS BOND : angle 0.62595 / 0.36 ( 6) hydrogen bonds : bond 0.03316 / 2.20 ( 425) hydrogen bonds : angle 3.98621 / 2.84 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8078 (mm-30) REVERT: R 174 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7364 (mm) REVERT: R 181 MET cc_start: 0.8169 (ttm) cc_final: 0.7618 (mtp) REVERT: R 192 ARG cc_start: 0.7525 (mmt-90) cc_final: 0.6679 (mmp-170) REVERT: R 193 LEU cc_start: 0.7533 (mt) cc_final: 0.7273 (tt) REVERT: R 289 ARG cc_start: 0.7705 (mtp180) cc_final: 0.7202 (mtm180) REVERT: R 336 ARG cc_start: 0.6064 (mtt180) cc_final: 0.5301 (tpt170) REVERT: R 345 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7438 (t80) REVERT: A 15 ARG cc_start: 0.7260 (ttt90) cc_final: 0.6941 (ttt-90) REVERT: A 31 ARG cc_start: 0.8413 (mtm110) cc_final: 0.8025 (mtt-85) REVERT: A 47 SER cc_start: 0.8501 (m) cc_final: 0.8147 (p) REVERT: A 187 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8774 (p) REVERT: A 310 ASP cc_start: 0.8059 (t70) cc_final: 0.7790 (t0) REVERT: A 323 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.7246 (mtm110) REVERT: B 10 GLU cc_start: 0.8306 (tp30) cc_final: 0.8011 (tp30) REVERT: B 262 MET cc_start: 0.7470 (tpt) cc_final: 0.7163 (tpt) REVERT: B 264 TYR cc_start: 0.9145 (m-80) cc_final: 0.8909 (m-80) REVERT: N 87 LYS cc_start: 0.7941 (mttt) cc_final: 0.7704 (ttmt) REVERT: N 90 ASP cc_start: 0.8484 (t0) cc_final: 0.8240 (t0) REVERT: N 114 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7746 (t) REVERT: N 117 TYR cc_start: 0.8540 (m-10) cc_final: 0.7888 (m-80) outliers start: 26 outliers final: 13 residues processed: 174 average time/residue: 0.1087 time to fit residues: 24.3550 Evaluate side-chains 161 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 268 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.208343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164751 restraints weight = 8940.534| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.63 r_work: 0.3392 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8968 Z= 0.170 Angle : 0.524 10.183 12176 Z= 0.268 Chirality : 0.040 0.137 1369 Planarity : 0.004 0.048 1514 Dihedral : 4.166 23.800 1246 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.60 % Allowed : 12.23 % Favored : 85.17 % 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: 0.58 (0.26), residues: 1050 helix: 2.10 (0.25), residues: 436 sheet: -0.60 (0.33), residues: 232 loop : -0.97 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 314 TYR 0.016 0.002 TYR R 392 PHE 0.018 0.002 PHE R 379 TRP 0.015 0.001 TRP N 47 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 8965) covalent geometry : angle 0.52409 / 0.27 (12170) SS BOND : bond 0.00169 / 0.09 ( 3) SS BOND : angle 0.64701 / 0.38 ( 6) hydrogen bonds : bond 0.03484 / 2.30 ( 425) hydrogen bonds : angle 4.00955 / 2.85 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8414 (tmm) cc_final: 0.7090 (mmm) REVERT: R 174 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7457 (mm) REVERT: R 181 MET cc_start: 0.8261 (ttm) cc_final: 0.7742 (mtp) REVERT: R 183 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6627 (ttm-80) REVERT: R 192 ARG cc_start: 0.7496 (mmt-90) cc_final: 0.6816 (mmp-170) REVERT: R 289 ARG cc_start: 0.7665 (mtp180) cc_final: 0.7211 (mtm180) REVERT: R 336 ARG cc_start: 0.6137 (mtt180) cc_final: 0.5460 (tpt170) REVERT: R 345 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7648 (t80) REVERT: A 15 ARG cc_start: 0.7267 (ttt90) cc_final: 0.7047 (ttt-90) REVERT: A 31 ARG cc_start: 0.8491 (mtm110) cc_final: 0.8215 (mtt-85) REVERT: A 187 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8763 (p) REVERT: A 274 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7661 (ptpp) REVERT: A 310 ASP cc_start: 0.8117 (t70) cc_final: 0.7870 (t0) REVERT: A 323 ARG cc_start: 0.7712 (mtm-85) cc_final: 0.7316 (mtm110) REVERT: B 10 GLU cc_start: 0.8371 (tp30) cc_final: 0.8052 (tp30) REVERT: B 262 MET cc_start: 0.7540 (tpt) cc_final: 0.7279 (tpt) REVERT: B 264 TYR cc_start: 0.9128 (m-80) cc_final: 0.8910 (m-80) REVERT: B 292 PHE cc_start: 0.8717 (m-10) cc_final: 0.8494 (m-80) REVERT: N 87 LYS cc_start: 0.7942 (mttt) cc_final: 0.7711 (ttmt) REVERT: N 90 ASP cc_start: 0.8488 (t0) cc_final: 0.8241 (t0) outliers start: 24 outliers final: 15 residues processed: 173 average time/residue: 0.1049 time to fit residues: 23.4183 Evaluate side-chains 164 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 77 optimal weight: 0.0770 chunk 18 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.209078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158245 restraints weight = 8864.643| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.78 r_work: 0.3521 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8968 Z= 0.120 Angle : 0.492 9.645 12176 Z= 0.251 Chirality : 0.039 0.134 1369 Planarity : 0.003 0.038 1514 Dihedral : 4.015 20.860 1246 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.81 % Allowed : 13.53 % Favored : 83.66 % 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: 0.74 (0.26), residues: 1050 helix: 2.29 (0.25), residues: 435 sheet: -0.49 (0.33), residues: 228 loop : -0.96 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 314 TYR 0.017 0.001 TYR R 141 PHE 0.013 0.001 PHE A 189 TRP 0.013 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 8965) covalent geometry : angle 0.49229 / 0.25 (12170) SS BOND : bond 0.00208 / 0.11 ( 3) SS BOND : angle 0.55282 / 0.32 ( 6) hydrogen bonds : bond 0.03200 / 2.12 ( 425) hydrogen bonds : angle 3.87341 / 2.75 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8393 (tmm) cc_final: 0.7065 (mmm) REVERT: R 174 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7520 (mm) REVERT: R 181 MET cc_start: 0.8327 (ttm) cc_final: 0.7821 (mtp) REVERT: R 183 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6734 (ttm-80) REVERT: R 192 ARG cc_start: 0.7526 (mmt-90) cc_final: 0.6873 (mmp-170) REVERT: R 289 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7230 (mtm180) REVERT: R 336 ARG cc_start: 0.6103 (mtt180) cc_final: 0.5414 (tpt170) REVERT: R 345 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7627 (t80) REVERT: A 15 ARG cc_start: 0.7287 (ttt90) cc_final: 0.7011 (ttt-90) REVERT: A 31 ARG cc_start: 0.8544 (mtm110) cc_final: 0.8197 (mtt-85) REVERT: A 47 SER cc_start: 0.8610 (m) cc_final: 0.8179 (p) REVERT: A 187 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8813 (p) REVERT: A 274 LYS cc_start: 0.8100 (ptpt) cc_final: 0.7630 (ptpp) REVERT: A 310 ASP cc_start: 0.8273 (t70) cc_final: 0.8036 (t0) REVERT: B 10 GLU cc_start: 0.8398 (tp30) cc_final: 0.8056 (tp30) REVERT: B 262 MET cc_start: 0.7691 (tpt) cc_final: 0.7463 (tpt) REVERT: B 264 TYR cc_start: 0.9112 (m-80) cc_final: 0.8906 (m-80) REVERT: G 47 GLU cc_start: 0.7466 (mp0) cc_final: 0.7244 (mp0) REVERT: N 90 ASP cc_start: 0.8517 (t0) cc_final: 0.7707 (t0) REVERT: N 117 TYR cc_start: 0.8548 (m-10) cc_final: 0.7941 (m-80) outliers start: 26 outliers final: 18 residues processed: 172 average time/residue: 0.1061 time to fit residues: 23.6162 Evaluate side-chains 170 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.208647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154051 restraints weight = 8933.094| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.23 r_work: 0.3474 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8968 Z= 0.134 Angle : 0.504 9.163 12176 Z= 0.255 Chirality : 0.039 0.190 1369 Planarity : 0.003 0.037 1514 Dihedral : 3.968 19.809 1246 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.81 % Allowed : 13.53 % Favored : 83.66 % 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: 0.77 (0.27), residues: 1050 helix: 2.31 (0.25), residues: 436 sheet: -0.53 (0.33), residues: 229 loop : -0.93 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 314 TYR 0.017 0.001 TYR R 141 PHE 0.020 0.001 PHE R 379 TRP 0.013 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 8965) covalent geometry : angle 0.50325 / 0.25 (12170) SS BOND : bond 0.00257 / 0.13 ( 3) SS BOND : angle 1.24230 / 0.99 ( 6) hydrogen bonds : bond 0.03171 / 2.09 ( 425) hydrogen bonds : angle 3.85757 / 2.74 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8463 (tmm) cc_final: 0.7095 (mmm) REVERT: R 174 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7385 (mm) REVERT: R 181 MET cc_start: 0.8304 (ttm) cc_final: 0.7748 (mtp) REVERT: R 183 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6560 (ttm-80) REVERT: R 192 ARG cc_start: 0.7447 (mmt-90) cc_final: 0.6661 (mmp-170) REVERT: R 194 LEU cc_start: 0.7339 (pt) cc_final: 0.7084 (tp) REVERT: R 289 ARG cc_start: 0.7543 (mtp180) cc_final: 0.7159 (mtm180) REVERT: R 336 ARG cc_start: 0.6138 (mtt180) cc_final: 0.5478 (tpt170) REVERT: R 345 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7648 (t80) REVERT: A 15 ARG cc_start: 0.7248 (ttt90) cc_final: 0.6961 (ttt-90) REVERT: A 31 ARG cc_start: 0.8563 (mtm110) cc_final: 0.8136 (mtt-85) REVERT: A 47 SER cc_start: 0.8604 (m) cc_final: 0.8147 (p) REVERT: A 187 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8765 (p) REVERT: A 274 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7647 (ptpp) REVERT: A 310 ASP cc_start: 0.8244 (t70) cc_final: 0.7982 (t0) REVERT: A 323 ARG cc_start: 0.7643 (mtm110) cc_final: 0.7178 (mmm160) REVERT: B 10 GLU cc_start: 0.8405 (tp30) cc_final: 0.8087 (tp30) REVERT: B 262 MET cc_start: 0.7774 (tpt) cc_final: 0.7510 (tpt) REVERT: G 47 GLU cc_start: 0.7473 (mp0) cc_final: 0.7182 (mp0) REVERT: N 82 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7355 (tp-100) REVERT: N 90 ASP cc_start: 0.8468 (t0) cc_final: 0.7607 (t0) outliers start: 26 outliers final: 18 residues processed: 164 average time/residue: 0.1052 time to fit residues: 22.2748 Evaluate side-chains 168 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 89 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.208480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.155657 restraints weight = 8930.497| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.92 r_work: 0.3471 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8968 Z= 0.143 Angle : 0.543 10.927 12176 Z= 0.272 Chirality : 0.040 0.263 1369 Planarity : 0.003 0.041 1514 Dihedral : 4.082 29.253 1246 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.81 % Allowed : 13.85 % Favored : 83.33 % 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: 0.82 (0.27), residues: 1050 helix: 2.35 (0.25), residues: 437 sheet: -0.45 (0.33), residues: 228 loop : -0.93 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 314 TYR 0.017 0.001 TYR R 141 PHE 0.014 0.001 PHE A 189 TRP 0.013 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 8965) covalent geometry : angle 0.53273 / 0.27 (12170) SS BOND : bond 0.00219 / 0.11 ( 3) SS BOND : angle 4.76032 / 2.75 ( 6) hydrogen bonds : bond 0.03173 / 2.09 ( 425) hydrogen bonds : angle 3.84619 / 2.72 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8384 (tmm) cc_final: 0.7090 (mmm) REVERT: R 174 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7491 (mm) REVERT: R 181 MET cc_start: 0.8238 (ttm) cc_final: 0.7762 (mtp) REVERT: R 183 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6647 (ttm-80) REVERT: R 192 ARG cc_start: 0.7521 (mmt-90) cc_final: 0.6792 (mmp-170) REVERT: R 194 LEU cc_start: 0.7223 (pt) cc_final: 0.6979 (tp) REVERT: R 289 ARG cc_start: 0.7398 (mtp180) cc_final: 0.7155 (mtm180) REVERT: R 336 ARG cc_start: 0.6254 (mtt180) cc_final: 0.5572 (tpt170) REVERT: R 345 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7861 (t80) REVERT: A 187 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8725 (p) REVERT: A 274 LYS cc_start: 0.8127 (ptpt) cc_final: 0.7773 (ptpp) REVERT: A 310 ASP cc_start: 0.8099 (t70) cc_final: 0.7899 (t0) REVERT: A 323 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7392 (mmm160) REVERT: B 10 GLU cc_start: 0.8385 (tp30) cc_final: 0.8035 (tp30) REVERT: B 262 MET cc_start: 0.7470 (tpt) cc_final: 0.7258 (tpt) REVERT: N 82 GLN cc_start: 0.8064 (tp-100) cc_final: 0.7518 (tp-100) outliers start: 26 outliers final: 19 residues processed: 161 average time/residue: 0.1054 time to fit residues: 22.0255 Evaluate side-chains 167 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.0060 chunk 28 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 40 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.208798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156962 restraints weight = 8888.264| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.78 r_work: 0.3521 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8968 Z= 0.130 Angle : 0.523 8.251 12176 Z= 0.265 Chirality : 0.039 0.158 1369 Planarity : 0.003 0.036 1514 Dihedral : 4.029 29.656 1246 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.60 % Allowed : 14.18 % Favored : 83.23 % 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: 0.89 (0.27), residues: 1050 helix: 2.44 (0.25), residues: 436 sheet: -0.45 (0.33), residues: 229 loop : -0.91 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 314 TYR 0.017 0.001 TYR R 141 PHE 0.022 0.001 PHE R 379 TRP 0.012 0.001 TRP N 47 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 8965) covalent geometry : angle 0.51725 / 0.26 (12170) SS BOND : bond 0.00184 / 0.10 ( 3) SS BOND : angle 3.39415 / 2.12 ( 6) hydrogen bonds : bond 0.03081 / 2.03 ( 425) hydrogen bonds : angle 3.79355 / 2.68 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8508 (tmm) cc_final: 0.7219 (mmm) REVERT: R 174 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7615 (mm) REVERT: R 181 MET cc_start: 0.8433 (ttm) cc_final: 0.7928 (mtp) REVERT: R 183 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6735 (ttm-80) REVERT: R 192 ARG cc_start: 0.7539 (mmt-90) cc_final: 0.6800 (mmp-170) REVERT: R 194 LEU cc_start: 0.7305 (pt) cc_final: 0.7001 (tp) REVERT: R 289 ARG cc_start: 0.7413 (mtp180) cc_final: 0.7145 (mtm180) REVERT: R 336 ARG cc_start: 0.6365 (mtt180) cc_final: 0.5487 (tpt170) REVERT: R 345 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.7910 (t80) REVERT: A 47 SER cc_start: 0.8629 (m) cc_final: 0.8213 (p) REVERT: A 187 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8762 (p) REVERT: A 274 LYS cc_start: 0.8115 (ptpt) cc_final: 0.7739 (ptpp) REVERT: A 323 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7397 (mmm160) REVERT: B 10 GLU cc_start: 0.8432 (tp30) cc_final: 0.8135 (tp30) REVERT: B 258 ASP cc_start: 0.8095 (t70) cc_final: 0.7198 (t0) REVERT: G 17 GLU cc_start: 0.8359 (tp30) cc_final: 0.7949 (tt0) REVERT: N 82 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7552 (tp-100) REVERT: N 117 TYR cc_start: 0.8559 (m-10) cc_final: 0.7978 (m-80) outliers start: 24 outliers final: 18 residues processed: 166 average time/residue: 0.1058 time to fit residues: 22.7410 Evaluate side-chains 165 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 0.0270 chunk 12 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.209300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157642 restraints weight = 8918.835| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.81 r_work: 0.3513 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8968 Z= 0.119 Angle : 0.515 7.945 12176 Z= 0.262 Chirality : 0.039 0.134 1369 Planarity : 0.003 0.035 1514 Dihedral : 3.972 29.152 1246 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.27 % Allowed : 14.83 % Favored : 82.90 % 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 (0.27), residues: 1050 helix: 2.48 (0.25), residues: 437 sheet: -0.47 (0.33), residues: 230 loop : -0.93 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 314 TYR 0.017 0.001 TYR R 141 PHE 0.013 0.001 PHE A 189 TRP 0.011 0.001 TRP N 47 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8965) covalent geometry : angle 0.51065 / 0.26 (12170) SS BOND : bond 0.00216 / 0.11 ( 3) SS BOND : angle 2.94390 / 1.92 ( 6) hydrogen bonds : bond 0.03015 / 1.97 ( 425) hydrogen bonds : angle 3.73011 / 2.63 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8481 (tmm) cc_final: 0.7212 (mmm) REVERT: R 174 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7507 (mm) REVERT: R 181 MET cc_start: 0.8330 (ttm) cc_final: 0.7853 (mtp) REVERT: R 183 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6720 (ttm-80) REVERT: R 192 ARG cc_start: 0.7486 (mmt-90) cc_final: 0.6779 (mmp-170) REVERT: R 194 LEU cc_start: 0.7300 (pt) cc_final: 0.6985 (tp) REVERT: R 336 ARG cc_start: 0.6332 (mtt180) cc_final: 0.5432 (tpt170) REVERT: R 345 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7860 (t80) REVERT: A 47 SER cc_start: 0.8600 (m) cc_final: 0.8178 (p) REVERT: A 323 ARG cc_start: 0.7745 (mtm110) cc_final: 0.7350 (mmm160) REVERT: A 353 MET cc_start: 0.8347 (tmm) cc_final: 0.7957 (tmm) REVERT: B 10 GLU cc_start: 0.8411 (tp30) cc_final: 0.8056 (tp30) REVERT: B 175 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: B 322 ASP cc_start: 0.8061 (m-30) cc_final: 0.7501 (m-30) REVERT: G 17 GLU cc_start: 0.8308 (tp30) cc_final: 0.7919 (tt0) REVERT: N 82 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7493 (tp-100) REVERT: N 117 TYR cc_start: 0.8543 (m-10) cc_final: 0.7963 (m-80) outliers start: 21 outliers final: 16 residues processed: 160 average time/residue: 0.0963 time to fit residues: 20.1068 Evaluate side-chains 161 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 49 optimal weight: 0.0370 chunk 91 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.209475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159090 restraints weight = 8840.027| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.72 r_work: 0.3506 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8968 Z= 0.117 Angle : 0.519 7.595 12176 Z= 0.265 Chirality : 0.039 0.133 1369 Planarity : 0.003 0.035 1514 Dihedral : 3.945 28.676 1246 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.16 % Allowed : 15.26 % Favored : 82.58 % 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: 0.97 (0.27), residues: 1050 helix: 2.57 (0.25), residues: 437 sheet: -0.46 (0.33), residues: 230 loop : -0.92 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 314 TYR 0.017 0.001 TYR R 141 PHE 0.012 0.001 PHE B 199 TRP 0.011 0.001 TRP N 47 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8965) covalent geometry : angle 0.51551 / 0.26 (12170) SS BOND : bond 0.00185 / 0.10 ( 3) SS BOND : angle 2.75125 / 1.82 ( 6) hydrogen bonds : bond 0.02956 / 1.94 ( 425) hydrogen bonds : angle 3.70076 / 2.62 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.35 seconds wall clock time: 38 minutes 40.21 seconds (2320.21 seconds total)