Starting phenix.real_space_refine on Tue Mar 3 22:21:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vab_31836/03_2026/7vab_31836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vab_31836/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vab_31836/03_2026/7vab_31836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vab_31836/03_2026/7vab_31836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vab_31836/03_2026/7vab_31836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vab_31836/03_2026/7vab_31836.map" } 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-5986/lib/python3.9/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: 2.16, per 1000 atoms: 0.25 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: 0.69 Conformation dependent library (CDL) restraints added in 324.7 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: 0.29 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: 1.51 Time building geometry restraints manager: 0.95 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: 5379 14.99 - 29.98: 158 29.98 - 44.98: 52 44.98 - 59.97: 16 59.97 - 74.96: 6 Dihedral angle restraints: 5611 sinusoidal: 2484 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 5608 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.040 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 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 : 9.193 74.961 3582 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 covalent geometry : bond 0.00350 ( 8965) covalent geometry : angle 0.80018 (12170) SS BOND : bond 0.00190 ( 3) SS BOND : angle 1.98691 ( 6) hydrogen bonds : bond 0.14833 ( 425) hydrogen bonds : angle 6.60614 ( 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 : 0.316 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: 0.1358 time to fit residues: 46.5220 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 : 0.334 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4325 r_free = 0.4325 target = 0.212908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.165636 restraints weight = 8965.158| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.30 r_work: 0.3447 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2456 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= 0.161 Angle : 0.566 15.098 12176 Z= 0.288 Chirality : 0.041 0.147 1369 Planarity : 0.004 0.051 1514 Dihedral : 6.732 59.921 1582 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.19 % Allowed : 8.66 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1050 helix: 0.90 (0.24), residues: 432 sheet: -0.51 (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 0.027 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 covalent geometry : bond 0.00376 ( 8965) covalent geometry : angle 0.56526 (12170) SS BOND : bond 0.00357 ( 3) SS BOND : angle 1.00208 ( 6) hydrogen bonds : bond 0.04028 ( 425) hydrogen bonds : angle 4.46095 ( 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 199 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7907 (mm-30) REVERT: R 174 ILE cc_start: 0.7593 (mt) cc_final: 0.7227 (mm) REVERT: R 181 MET cc_start: 0.8240 (ttm) cc_final: 0.7935 (mtt) REVERT: R 192 ARG cc_start: 0.7260 (mmt-90) cc_final: 0.6545 (mmp-170) REVERT: R 193 LEU cc_start: 0.7753 (mt) cc_final: 0.7399 (tt) REVERT: R 252 GLU cc_start: 0.5220 (mp0) cc_final: 0.4591 (pt0) REVERT: R 253 GLU cc_start: 0.4838 (pm20) cc_final: 0.4328 (mm-30) REVERT: R 289 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7325 (mtm180) REVERT: R 336 ARG cc_start: 0.6037 (mtt180) cc_final: 0.5380 (tpt170) REVERT: R 345 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 31 ARG cc_start: 0.8234 (mtm110) cc_final: 0.7906 (mtt-85) REVERT: A 259 ASN cc_start: 0.8649 (t0) cc_final: 0.8430 (t0) REVERT: A 274 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7805 (ptpp) REVERT: A 310 ASP cc_start: 0.8038 (t70) cc_final: 0.7743 (t0) REVERT: A 323 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7210 (mmm160) REVERT: B 44 GLN cc_start: 0.8194 (mt0) cc_final: 0.7944 (mm-40) REVERT: B 217 MET cc_start: 0.7959 (mtm) cc_final: 0.7254 (mmt) REVERT: N 87 LYS cc_start: 0.7988 (mttt) cc_final: 0.7659 (ttmt) REVERT: N 90 ASP cc_start: 0.8514 (t0) cc_final: 0.8243 (t0) outliers start: 11 outliers final: 6 residues processed: 196 average time/residue: 0.1299 time to fit residues: 32.9060 Evaluate side-chains 165 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 0.5980 chunk 34 optimal weight: 0.4980 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 0.0570 chunk 16 optimal weight: 0.3980 chunk 2 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4329 r_free = 0.4329 target = 0.213824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155584 restraints weight = 8945.250| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.32 r_work: 0.3506 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8968 Z= 0.128 Angle : 0.516 12.830 12176 Z= 0.261 Chirality : 0.040 0.140 1369 Planarity : 0.003 0.036 1514 Dihedral : 6.166 49.139 1582 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.27 % Allowed : 10.93 % Favored : 86.80 % 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: 0.23 (0.26), residues: 1050 helix: 1.65 (0.25), residues: 433 sheet: -0.44 (0.33), residues: 231 loop : -1.16 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 314 TYR 0.021 0.002 TYR R 392 PHE 0.020 0.002 PHE R 386 TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8965) covalent geometry : angle 0.51626 (12170) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.65281 ( 6) hydrogen bonds : bond 0.03494 ( 425) hydrogen bonds : angle 4.11109 ( 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 184 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7987 (mm-30) REVERT: R 181 MET cc_start: 0.8334 (ttm) cc_final: 0.7815 (mtp) REVERT: R 192 ARG cc_start: 0.7380 (mmt-90) cc_final: 0.6559 (mmp-170) REVERT: R 193 LEU cc_start: 0.7668 (mt) cc_final: 0.7404 (tt) REVERT: R 237 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: R 289 ARG cc_start: 0.7750 (mtp180) cc_final: 0.7258 (mtm180) REVERT: R 336 ARG cc_start: 0.6027 (mtt180) cc_final: 0.5272 (tpt170) REVERT: R 345 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7383 (t80) REVERT: A 15 ARG cc_start: 0.7222 (ttt90) cc_final: 0.6750 (ttt-90) REVERT: A 31 ARG cc_start: 0.8411 (mtm110) cc_final: 0.8099 (mtt-85) REVERT: A 47 SER cc_start: 0.8570 (m) cc_final: 0.8302 (p) REVERT: A 310 ASP cc_start: 0.8249 (t70) cc_final: 0.7992 (t0) REVERT: A 323 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7193 (mmm160) REVERT: B 262 MET cc_start: 0.7553 (tpt) cc_final: 0.7237 (tpt) REVERT: B 264 TYR cc_start: 0.9174 (m-80) cc_final: 0.8680 (m-80) REVERT: N 87 LYS cc_start: 0.8000 (mttt) cc_final: 0.7667 (ttmt) REVERT: N 90 ASP cc_start: 0.8526 (t0) cc_final: 0.8288 (t0) REVERT: N 117 TYR cc_start: 0.8646 (m-10) cc_final: 0.8023 (m-80) outliers start: 21 outliers final: 13 residues processed: 179 average time/residue: 0.1315 time to fit residues: 30.1668 Evaluate side-chains 165 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 271 VAL 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 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 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: 0.8980 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.211206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.163546 restraints weight = 8987.383| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.25 r_work: 0.3437 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8968 Z= 0.132 Angle : 0.501 11.246 12176 Z= 0.255 Chirality : 0.040 0.137 1369 Planarity : 0.003 0.043 1514 Dihedral : 5.802 43.940 1582 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.60 % Allowed : 11.36 % 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: 0.52 (0.26), residues: 1050 helix: 2.04 (0.25), residues: 433 sheet: -0.34 (0.33), residues: 223 loop : -1.16 (0.30), residues: 394 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 0.005 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8965) covalent geometry : angle 0.50043 (12170) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.63692 ( 6) hydrogen bonds : bond 0.03320 ( 425) hydrogen bonds : angle 3.98015 ( 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 173 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8046 (mm-30) REVERT: R 174 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7470 (mm) REVERT: R 181 MET cc_start: 0.8139 (ttm) cc_final: 0.7619 (mtp) REVERT: R 192 ARG cc_start: 0.7375 (mmt-90) cc_final: 0.6580 (mmp-170) REVERT: R 193 LEU cc_start: 0.7661 (mt) cc_final: 0.7375 (tt) REVERT: R 289 ARG cc_start: 0.7718 (mtp180) cc_final: 0.7213 (mtm180) REVERT: R 336 ARG cc_start: 0.6047 (mtt180) cc_final: 0.5351 (tpt170) REVERT: R 345 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7441 (t80) REVERT: A 15 ARG cc_start: 0.7272 (ttt90) cc_final: 0.6939 (ttt-90) REVERT: A 31 ARG cc_start: 0.8389 (mtm110) cc_final: 0.8031 (mtt-85) REVERT: A 47 SER cc_start: 0.8552 (m) cc_final: 0.8252 (p) REVERT: A 187 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8748 (p) REVERT: A 193 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7919 (mtmm) REVERT: A 310 ASP cc_start: 0.8032 (t70) cc_final: 0.7785 (t0) REVERT: A 323 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7280 (mtm110) REVERT: B 262 MET cc_start: 0.7367 (tpt) cc_final: 0.7042 (tpt) REVERT: N 90 ASP cc_start: 0.8509 (t0) cc_final: 0.8273 (t0) REVERT: N 114 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7758 (t) REVERT: N 117 TYR cc_start: 0.8574 (m-10) cc_final: 0.7935 (m-80) outliers start: 24 outliers final: 16 residues processed: 168 average time/residue: 0.1393 time to fit residues: 29.8012 Evaluate side-chains 162 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 315 ILE 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 195 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 334 SER 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: 2.9990 chunk 56 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.208022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.162985 restraints weight = 8935.821| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.95 r_work: 0.3358 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8968 Z= 0.177 Angle : 0.531 9.577 12176 Z= 0.272 Chirality : 0.041 0.138 1369 Planarity : 0.004 0.042 1514 Dihedral : 5.588 42.927 1582 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.92 % Allowed : 12.12 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 1050 helix: 2.09 (0.25), residues: 437 sheet: -0.53 (0.33), residues: 232 loop : -1.03 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 314 TYR 0.016 0.002 TYR R 141 PHE 0.017 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 covalent geometry : bond 0.00418 ( 8965) covalent geometry : angle 0.53101 (12170) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.67909 ( 6) hydrogen bonds : bond 0.03501 ( 425) hydrogen bonds : angle 4.03421 ( 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 178 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8078 (mm-30) REVERT: R 140 MET cc_start: 0.8471 (tmm) cc_final: 0.7096 (mmm) REVERT: R 174 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7411 (mm) REVERT: R 181 MET cc_start: 0.8287 (ttm) cc_final: 0.7752 (mtp) REVERT: R 183 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6514 (ttm-80) REVERT: R 192 ARG cc_start: 0.7487 (mmt-90) cc_final: 0.6730 (mmp-170) REVERT: R 289 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7154 (mtm180) REVERT: R 336 ARG cc_start: 0.6105 (mtt180) cc_final: 0.5344 (tpt170) REVERT: R 345 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7610 (t80) REVERT: A 15 ARG cc_start: 0.7252 (ttt90) cc_final: 0.7003 (ttt-90) REVERT: A 20 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7298 (mm-30) REVERT: A 31 ARG cc_start: 0.8528 (mtm110) cc_final: 0.8208 (mtt-85) REVERT: A 47 SER cc_start: 0.8619 (m) cc_final: 0.8174 (p) REVERT: A 187 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8776 (p) REVERT: A 193 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7979 (mtmm) REVERT: A 274 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7632 (ptpp) REVERT: A 310 ASP cc_start: 0.8159 (t70) cc_final: 0.7903 (t0) REVERT: A 323 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7331 (mtm110) REVERT: B 262 MET cc_start: 0.7637 (tpt) cc_final: 0.7371 (tpt) REVERT: B 264 TYR cc_start: 0.9182 (m-80) cc_final: 0.8914 (m-80) REVERT: N 90 ASP cc_start: 0.8567 (t0) cc_final: 0.8281 (t0) REVERT: N 114 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7820 (t) outliers start: 27 outliers final: 16 residues processed: 169 average time/residue: 0.1384 time to fit residues: 29.7529 Evaluate side-chains 164 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 206 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.209291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157587 restraints weight = 8894.035| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.91 r_work: 0.3501 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8968 Z= 0.120 Angle : 0.488 10.728 12176 Z= 0.248 Chirality : 0.039 0.136 1369 Planarity : 0.003 0.038 1514 Dihedral : 5.294 40.105 1582 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.92 % Allowed : 12.77 % Favored : 84.31 % 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: 2.24 (0.25), residues: 437 sheet: -0.46 (0.33), residues: 229 loop : -0.93 (0.31), residues: 384 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 0.012 0.001 TRP N 47 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8965) covalent geometry : angle 0.48760 (12170) SS BOND : bond 0.00230 ( 3) SS BOND : angle 0.57594 ( 6) hydrogen bonds : bond 0.03159 ( 425) hydrogen bonds : angle 3.84972 ( 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 186 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8276 (tmm) cc_final: 0.7052 (mmm) REVERT: R 174 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7504 (mm) REVERT: R 181 MET cc_start: 0.8196 (ttm) cc_final: 0.7781 (mtp) REVERT: R 183 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6715 (ttm-80) REVERT: R 192 ARG cc_start: 0.7562 (mmt-90) cc_final: 0.6911 (mmp-170) REVERT: R 289 ARG cc_start: 0.7497 (mtp180) cc_final: 0.7210 (mtm180) REVERT: R 336 ARG cc_start: 0.6155 (mtt180) cc_final: 0.5530 (tpt170) REVERT: R 345 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7709 (t80) REVERT: A 15 ARG cc_start: 0.7280 (ttt90) cc_final: 0.7038 (ttt-90) REVERT: A 47 SER cc_start: 0.8579 (m) cc_final: 0.8204 (p) REVERT: A 274 LYS cc_start: 0.8115 (ptpt) cc_final: 0.7671 (ptpp) REVERT: A 323 ARG cc_start: 0.7626 (mtm-85) cc_final: 0.7362 (mtm110) REVERT: B 264 TYR cc_start: 0.9032 (m-80) cc_final: 0.8814 (m-80) REVERT: N 90 ASP cc_start: 0.8380 (t0) cc_final: 0.8108 (t0) REVERT: N 117 TYR cc_start: 0.8487 (m-10) cc_final: 0.7877 (m-80) outliers start: 27 outliers final: 14 residues processed: 176 average time/residue: 0.1344 time to fit residues: 30.2063 Evaluate side-chains 166 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN 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: 0.0770 chunk 64 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.209608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.148235 restraints weight = 8922.776| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.00 r_work: 0.3492 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3890 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= 0.116 Angle : 0.497 9.271 12176 Z= 0.253 Chirality : 0.039 0.185 1369 Planarity : 0.003 0.036 1514 Dihedral : 5.123 38.244 1582 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.71 % Allowed : 13.20 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.31 (0.25), residues: 439 sheet: -0.43 (0.33), residues: 229 loop : -0.92 (0.31), residues: 382 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 0.021 0.001 PHE R 379 TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8965) covalent geometry : angle 0.49717 (12170) SS BOND : bond 0.00193 ( 3) SS BOND : angle 0.57857 ( 6) hydrogen bonds : bond 0.03088 ( 425) hydrogen bonds : angle 3.77338 ( 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 180 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8553 (tmm) cc_final: 0.7180 (mmm) REVERT: R 174 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7255 (mm) REVERT: R 181 MET cc_start: 0.8295 (ttm) cc_final: 0.7754 (mtp) REVERT: R 183 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6562 (ttm-80) REVERT: R 192 ARG cc_start: 0.7441 (mmt-90) cc_final: 0.6675 (mmp-170) REVERT: R 289 ARG cc_start: 0.7606 (mtp180) cc_final: 0.7105 (mtm180) REVERT: R 336 ARG cc_start: 0.6063 (mtt180) cc_final: 0.5392 (tpt170) REVERT: R 345 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7596 (t80) REVERT: A 47 SER cc_start: 0.8577 (m) cc_final: 0.8149 (p) REVERT: A 274 LYS cc_start: 0.8067 (ptpt) cc_final: 0.7659 (ptpp) REVERT: A 323 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7235 (mtm110) REVERT: B 255 LEU cc_start: 0.8710 (mp) cc_final: 0.8498 (mt) REVERT: B 264 TYR cc_start: 0.9222 (m-80) cc_final: 0.8985 (m-80) REVERT: N 90 ASP cc_start: 0.8569 (t0) cc_final: 0.8295 (t0) REVERT: N 114 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7923 (t) REVERT: N 117 TYR cc_start: 0.8565 (m-10) cc_final: 0.7935 (m-80) outliers start: 25 outliers final: 17 residues processed: 170 average time/residue: 0.1388 time to fit residues: 30.1018 Evaluate side-chains 169 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 270 PHE 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 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 218 CYS 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 Chi-restraints excluded: chain N residue 114 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: 3.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 0.0370 chunk 73 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.206763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.154772 restraints weight = 8926.557| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.66 r_work: 0.3492 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8968 Z= 0.195 Angle : 0.545 9.537 12176 Z= 0.280 Chirality : 0.041 0.139 1369 Planarity : 0.004 0.043 1514 Dihedral : 5.159 38.914 1582 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.38 % Allowed : 13.74 % Favored : 83.87 % 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: 0.79 (0.26), residues: 1050 helix: 2.28 (0.25), residues: 437 sheet: -0.54 (0.34), residues: 215 loop : -0.84 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 314 TYR 0.017 0.002 TYR R 392 PHE 0.015 0.002 PHE A 189 TRP 0.015 0.001 TRP N 47 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8965) covalent geometry : angle 0.54467 (12170) SS BOND : bond 0.00175 ( 3) SS BOND : angle 1.18136 ( 6) hydrogen bonds : bond 0.03484 ( 425) hydrogen bonds : angle 3.98864 ( 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 168 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8476 (tmm) cc_final: 0.7203 (mmm) REVERT: R 174 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7479 (mm) REVERT: R 181 MET cc_start: 0.8445 (ttm) cc_final: 0.7937 (mtp) REVERT: R 183 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6781 (ttm-80) REVERT: R 192 ARG cc_start: 0.7535 (mmt-90) cc_final: 0.6835 (mmp-170) REVERT: R 289 ARG cc_start: 0.7500 (mtp180) cc_final: 0.7191 (mtm180) REVERT: R 336 ARG cc_start: 0.6259 (mtt180) cc_final: 0.5601 (tpt170) REVERT: R 345 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7875 (t80) REVERT: A 274 LYS cc_start: 0.8151 (ptpt) cc_final: 0.7758 (ptpp) REVERT: B 258 ASP cc_start: 0.8177 (t70) cc_final: 0.7361 (t0) REVERT: G 17 GLU cc_start: 0.8346 (tp30) cc_final: 0.7955 (tt0) REVERT: N 82 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7547 (tp-100) REVERT: N 90 ASP cc_start: 0.8448 (t0) cc_final: 0.8043 (t0) outliers start: 22 outliers final: 16 residues processed: 160 average time/residue: 0.1341 time to fit residues: 27.5010 Evaluate side-chains 162 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 CYS 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: 0.7980 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 40 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.208576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.157008 restraints weight = 8878.797| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.76 r_work: 0.3510 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8968 Z= 0.129 Angle : 0.539 11.988 12176 Z= 0.272 Chirality : 0.040 0.250 1369 Planarity : 0.003 0.038 1514 Dihedral : 5.073 36.768 1582 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.38 % Allowed : 14.29 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 2.43 (0.25), residues: 436 sheet: -0.47 (0.33), residues: 229 loop : -0.88 (0.31), residues: 385 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 0.022 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 covalent geometry : bond 0.00298 ( 8965) covalent geometry : angle 0.52719 (12170) SS BOND : bond 0.00283 ( 3) SS BOND : angle 5.03114 ( 6) hydrogen bonds : bond 0.03155 ( 425) hydrogen bonds : angle 3.80594 ( 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 170 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8424 (tmm) cc_final: 0.7190 (mmm) REVERT: R 174 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7566 (mm) REVERT: R 181 MET cc_start: 0.8442 (ttm) cc_final: 0.7955 (mtp) REVERT: R 183 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6807 (ttm-80) REVERT: R 192 ARG cc_start: 0.7554 (mmt-90) cc_final: 0.6862 (mmp-170) REVERT: R 289 ARG cc_start: 0.7424 (mtp180) cc_final: 0.7119 (mtm180) REVERT: R 336 ARG cc_start: 0.6392 (mtt180) cc_final: 0.5624 (tpt170) REVERT: R 345 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7881 (t80) REVERT: A 274 LYS cc_start: 0.8109 (ptpt) cc_final: 0.7727 (ptpp) REVERT: A 323 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7315 (mmm160) REVERT: B 258 ASP cc_start: 0.8075 (t70) cc_final: 0.7220 (t0) REVERT: G 17 GLU cc_start: 0.8342 (tp30) cc_final: 0.7991 (tt0) REVERT: N 82 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7547 (tp-100) REVERT: N 90 ASP cc_start: 0.8515 (t0) cc_final: 0.8048 (m-30) outliers start: 22 outliers final: 18 residues processed: 161 average time/residue: 0.1373 time to fit residues: 28.2195 Evaluate side-chains 163 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 270 PHE 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 A residue 284 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 CYS 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: 10.0000 chunk 75 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.208428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155550 restraints weight = 8933.162| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.87 r_work: 0.3502 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8968 Z= 0.137 Angle : 0.530 8.380 12176 Z= 0.270 Chirality : 0.040 0.171 1369 Planarity : 0.003 0.038 1514 Dihedral : 5.040 36.404 1582 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.49 % Allowed : 14.50 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 2.43 (0.25), residues: 437 sheet: -0.51 (0.33), residues: 230 loop : -0.85 (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 0.014 0.001 PHE A 189 TRP 0.012 0.001 TRP N 47 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8965) covalent geometry : angle 0.52420 (12170) SS BOND : bond 0.00207 ( 3) SS BOND : angle 3.53215 ( 6) hydrogen bonds : bond 0.03133 ( 425) hydrogen bonds : angle 3.81646 ( 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 168 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8482 (tmm) cc_final: 0.7217 (mmm) REVERT: R 174 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7546 (mm) REVERT: R 181 MET cc_start: 0.8439 (ttm) cc_final: 0.7944 (mtp) REVERT: R 183 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6747 (ttm-80) REVERT: R 192 ARG cc_start: 0.7496 (mmt-90) cc_final: 0.6842 (mmp-170) REVERT: R 289 ARG cc_start: 0.7421 (mtp180) cc_final: 0.7069 (mtm180) REVERT: R 336 ARG cc_start: 0.6388 (mtt180) cc_final: 0.5479 (tpt170) REVERT: R 345 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7906 (t80) REVERT: A 20 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 47 SER cc_start: 0.8622 (m) cc_final: 0.8194 (p) REVERT: A 274 LYS cc_start: 0.8074 (ptpt) cc_final: 0.7700 (ptpp) REVERT: A 323 ARG cc_start: 0.7733 (mtm110) cc_final: 0.7393 (mmm160) REVERT: A 353 MET cc_start: 0.8410 (tmm) cc_final: 0.8040 (tmm) REVERT: B 258 ASP cc_start: 0.8078 (t70) cc_final: 0.7256 (t0) REVERT: G 17 GLU cc_start: 0.8341 (tp30) cc_final: 0.7969 (tt0) REVERT: N 82 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7546 (tp-100) REVERT: N 90 ASP cc_start: 0.8557 (t0) cc_final: 0.8123 (m-30) REVERT: N 117 TYR cc_start: 0.8545 (m-10) cc_final: 0.7975 (m-80) outliers start: 23 outliers final: 19 residues processed: 159 average time/residue: 0.1417 time to fit residues: 28.8298 Evaluate side-chains 163 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 270 PHE 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 A residue 284 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 21 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: 10.0000 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 0.0870 chunk 49 optimal weight: 0.4980 chunk 91 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 224 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.210373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158932 restraints weight = 8842.694| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.92 r_work: 0.3516 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8968 Z= 0.105 Angle : 0.502 7.850 12176 Z= 0.255 Chirality : 0.039 0.133 1369 Planarity : 0.003 0.038 1514 Dihedral : 4.887 37.240 1582 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.16 % Allowed : 14.72 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.27), residues: 1050 helix: 2.56 (0.25), residues: 438 sheet: -0.45 (0.33), residues: 229 loop : -0.86 (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 B 297 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8965) covalent geometry : angle 0.49760 (12170) SS BOND : bond 0.00245 ( 3) SS BOND : angle 3.04478 ( 6) hydrogen bonds : bond 0.02924 ( 425) hydrogen bonds : angle 3.67920 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.27 seconds wall clock time: 47 minutes 48.80 seconds (2868.80 seconds total)