Starting phenix.real_space_refine on Wed Feb 4 19:01:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mej_48215/02_2026/9mej_48215.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mej_48215/02_2026/9mej_48215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mej_48215/02_2026/9mej_48215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mej_48215/02_2026/9mej_48215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mej_48215/02_2026/9mej_48215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mej_48215/02_2026/9mej_48215.map" } resolution = 3.99 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= 0.002 sd= 0.022 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 71 5.16 5 C 8020 2.51 5 N 1985 2.21 5 O 2061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12137 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2277 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "B" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "C" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "D" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "E" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3014 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 18, 'TRANS': 352} Chain breaks: 2 Time building chain proxies: 2.81, per 1000 atoms: 0.23 Number of scatterers: 12137 At special positions: 0 Unit cell: (141.375, 107.3, 126.875, 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 71 16.00 O 2061 8.00 N 1985 7.00 C 8020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 186 " distance=2.04 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 55 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS E 216 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 226 " - pdb=" SG CYS E 238 " distance=2.03 Simple disulfide: pdb=" SG CYS E 294 " - pdb=" SG CYS E 326 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 436 " distance=2.03 Simple disulfide: pdb=" SG CYS E 386 " - pdb=" SG CYS E 409 " 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: 0.91 Conformation dependent library (CDL) restraints added in 577.1 milliseconds 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2862 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 64.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 36 through 64 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 72 through 89 removed outlier: 4.135A pdb=" N TYR A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.846A pdb=" N TRP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 139 removed outlier: 3.759A pdb=" N CYS A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 154 removed outlier: 3.737A pdb=" N LYS A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 192 through 208 removed outlier: 3.549A pdb=" N VAL A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 229 Processing helix chain 'A' and resid 237 through 267 removed outlier: 4.152A pdb=" N THR A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 273 through 292 removed outlier: 3.661A pdb=" N GLU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'B' and resid 35 through 64 Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 72 through 89 removed outlier: 4.150A pdb=" N TYR B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 100 removed outlier: 4.025A pdb=" N TRP B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 139 removed outlier: 3.686A pdb=" N CYS B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 154 through 167 removed outlier: 4.154A pdb=" N VAL B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Proline residue: B 163 - end of helix Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.759A pdb=" N VAL B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 227 removed outlier: 4.227A pdb=" N SER B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 266 removed outlier: 3.905A pdb=" N LEU B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 254 - end of helix removed outlier: 3.710A pdb=" N LEU B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 291 Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.738A pdb=" N ILE B 300 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 64 Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 72 through 100 removed outlier: 4.498A pdb=" N TYR C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Proline residue: C 92 - end of helix Processing helix chain 'C' and resid 106 through 139 removed outlier: 4.034A pdb=" N VAL C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 Processing helix chain 'C' and resid 154 through 167 removed outlier: 4.691A pdb=" N VAL C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 192 through 208 Processing helix chain 'C' and resid 208 through 227 Processing helix chain 'C' and resid 237 through 266 removed outlier: 4.120A pdb=" N THR C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 273 through 292 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.517A pdb=" N ILE C 300 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 64 Proline residue: D 42 - end of helix Processing helix chain 'D' and resid 72 through 89 removed outlier: 4.342A pdb=" N TYR D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 100 removed outlier: 3.614A pdb=" N TRP D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 139 removed outlier: 3.619A pdb=" N VAL D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 154 through 168 removed outlier: 4.456A pdb=" N VAL D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Proline residue: D 163 - end of helix Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 193 through 227 removed outlier: 5.674A pdb=" N LEU D 210 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Proline residue: D 211 - end of helix Processing helix chain 'D' and resid 238 through 266 Proline residue: D 254 - end of helix Processing helix chain 'D' and resid 273 through 292 Processing helix chain 'D' and resid 293 through 304 removed outlier: 3.741A pdb=" N LEU D 297 " --> pdb=" O PHE D 293 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN D 298 " --> pdb=" O HIS D 294 " (cutoff:3.500A) Proline residue: D 299 - end of helix Processing helix chain 'E' and resid 48 through 55 Processing helix chain 'E' and resid 78 through 96 removed outlier: 3.780A pdb=" N ILE E 96 " --> pdb=" O PHE E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 140 removed outlier: 3.765A pdb=" N ARG E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA E 139 " --> pdb=" O PRO E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 345 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 388 through 397 Processing helix chain 'E' and resid 461 through 469 removed outlier: 4.185A pdb=" N TYR E 465 " --> pdb=" O VAL E 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 179 removed outlier: 3.524A pdb=" N ILE A 185 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.869A pdb=" N ASN B 176 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 187 " --> pdb=" O ASN B 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.717A pdb=" N ASN C 176 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP C 187 " --> pdb=" O ASN C 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 175 through 177 removed outlier: 4.337A pdb=" N ASN D 176 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP D 187 " --> pdb=" O ASN D 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 34 through 35 removed outlier: 3.817A pdb=" N VAL E 241 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 56 through 57 removed outlier: 6.694A pdb=" N CYS E 42 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE E 41 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 213 " --> pdb=" O MET E 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 71 through 74 removed outlier: 6.435A pdb=" N GLU E 71 " --> pdb=" O ASN E 237 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN E 237 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AA9, first strand: chain 'E' and resid 259 through 260 removed outlier: 6.467A pdb=" N GLY E 259 " --> pdb=" O THR E 441 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 271 through 273 removed outlier: 4.009A pdb=" N SER E 438 " --> pdb=" O MET E 292 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP E 325 " --> pdb=" O LYS E 295 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS E 326 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 377 " --> pdb=" O LEU E 384 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 2124 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: 1.90 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3191 1.34 - 1.46: 3247 1.46 - 1.58: 5945 1.58 - 1.71: 0 1.71 - 1.83: 91 Bond restraints: 12474 Sorted by residual: bond pdb=" C ASP C 182 " pdb=" N ARG C 183 " ideal model delta sigma weight residual 1.335 1.214 0.121 1.25e-02 6.40e+03 9.36e+01 bond pdb=" N PRO B 299 " pdb=" CD PRO B 299 " ideal model delta sigma weight residual 1.473 1.580 -0.107 1.40e-02 5.10e+03 5.82e+01 bond pdb=" C ASN A 298 " pdb=" N PRO A 299 " ideal model delta sigma weight residual 1.336 1.379 -0.044 1.23e-02 6.61e+03 1.26e+01 bond pdb=" CA ILE D 162 " pdb=" CB ILE D 162 " ideal model delta sigma weight residual 1.534 1.552 -0.017 6.80e-03 2.16e+04 6.42e+00 bond pdb=" C ASN B 298 " pdb=" N PRO B 299 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.28e-02 6.10e+03 6.31e+00 ... (remaining 12469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.62: 16807 5.62 - 11.24: 146 11.24 - 16.86: 18 16.86 - 22.48: 5 22.48 - 28.10: 2 Bond angle restraints: 16978 Sorted by residual: angle pdb=" C ASP E 209 " pdb=" CA ASP E 209 " pdb=" CB ASP E 209 " ideal model delta sigma weight residual 110.79 82.69 28.10 1.63e+00 3.76e-01 2.97e+02 angle pdb=" N ALA E 210 " pdb=" CA ALA E 210 " pdb=" CB ALA E 210 " ideal model delta sigma weight residual 111.65 136.56 -24.91 1.58e+00 4.01e-01 2.49e+02 angle pdb=" N ARG C 183 " pdb=" CA ARG C 183 " pdb=" C ARG C 183 " ideal model delta sigma weight residual 111.11 121.57 -10.46 1.20e+00 6.94e-01 7.60e+01 angle pdb=" O ASP C 182 " pdb=" C ASP C 182 " pdb=" N ARG C 183 " ideal model delta sigma weight residual 122.59 112.24 10.35 1.33e+00 5.65e-01 6.06e+01 angle pdb=" CB MET C 205 " pdb=" CG MET C 205 " pdb=" SD MET C 205 " ideal model delta sigma weight residual 112.70 132.91 -20.21 3.00e+00 1.11e-01 4.54e+01 ... (remaining 16973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 6074 16.90 - 33.80: 915 33.80 - 50.69: 266 50.69 - 67.59: 42 67.59 - 84.49: 11 Dihedral angle restraints: 7308 sinusoidal: 2888 harmonic: 4420 Sorted by residual: dihedral pdb=" C ASP E 209 " pdb=" N ASP E 209 " pdb=" CA ASP E 209 " pdb=" CB ASP E 209 " ideal model delta harmonic sigma weight residual -122.60 -91.59 -31.01 0 2.50e+00 1.60e-01 1.54e+02 dihedral pdb=" N ALA E 210 " pdb=" C ALA E 210 " pdb=" CA ALA E 210 " pdb=" CB ALA E 210 " ideal model delta harmonic sigma weight residual 122.90 153.76 -30.86 0 2.50e+00 1.60e-01 1.52e+02 dihedral pdb=" CB CYS A 109 " pdb=" SG CYS A 109 " pdb=" SG CYS A 186 " pdb=" CB CYS A 186 " ideal model delta sinusoidal sigma weight residual 93.00 177.49 -84.49 1 1.00e+01 1.00e-02 8.68e+01 ... (remaining 7305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 1920 0.226 - 0.451: 14 0.451 - 0.677: 2 0.677 - 0.902: 2 0.902 - 1.128: 1 Chirality restraints: 1939 Sorted by residual: chirality pdb=" CA ALA E 210 " pdb=" N ALA E 210 " pdb=" C ALA E 210 " pdb=" CB ALA E 210 " both_signs ideal model delta sigma weight residual False 2.48 1.36 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ASP C 182 " pdb=" N ASP C 182 " pdb=" C ASP C 182 " pdb=" CB ASP C 182 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA ASN B 298 " pdb=" N ASN B 298 " pdb=" C ASN B 298 " pdb=" CB ASN B 298 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 1936 not shown) Planarity restraints: 2082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 298 " -0.067 5.00e-02 4.00e+02 9.44e-02 1.42e+01 pdb=" N PRO B 299 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 87 " -0.020 2.00e-02 2.50e+03 2.79e-02 1.36e+01 pdb=" CG PHE D 87 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE D 87 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE D 87 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE D 87 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 87 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 87 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 171 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" CG ASP B 171 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP B 171 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B 171 " -0.017 2.00e-02 2.50e+03 ... (remaining 2079 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 689 2.73 - 3.27: 11846 3.27 - 3.82: 21039 3.82 - 4.36: 23236 4.36 - 4.90: 39447 Nonbonded interactions: 96257 Sorted by model distance: nonbonded pdb=" O ASP E 209 " pdb=" CB ASP E 209 " model vdw 2.190 2.752 nonbonded pdb=" O VAL B 118 " pdb=" OG SER B 122 " model vdw 2.301 3.040 nonbonded pdb=" OD2 ASP E 87 " pdb=" OH TYR E 215 " model vdw 2.307 3.040 nonbonded pdb=" O ILE C 213 " pdb=" OG SER C 217 " model vdw 2.307 3.040 nonbonded pdb=" O LEU D 238 " pdb=" OG1 THR D 241 " model vdw 2.317 3.040 ... (remaining 96252 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 305) selection = (chain 'B' and resid 26 through 305) selection = (chain 'C' and resid 26 through 305) selection = (chain 'D' and resid 26 through 305) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.510 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.006 0.121 12485 Z= 0.283 Angle : 1.308 28.101 17000 Z= 0.651 Chirality : 0.076 1.128 1939 Planarity : 0.008 0.094 2082 Dihedral : 17.257 80.244 4413 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 0.83 % Allowed : 34.59 % Favored : 64.59 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.76 (0.19), residues: 1481 helix: -1.40 (0.15), residues: 921 sheet: -0.47 (0.51), residues: 97 loop : -2.77 (0.24), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 148 TYR 0.022 0.002 TYR D 302 PHE 0.064 0.002 PHE D 87 TRP 0.022 0.002 TRP C 94 HIS 0.006 0.001 HIS C 294 Details of bonding type rmsd covalent geometry : bond 0.00557 (12474) covalent geometry : angle 1.30779 (16978) SS BOND : bond 0.00270 ( 11) SS BOND : angle 1.46555 ( 22) hydrogen bonds : bond 0.12303 ( 716) hydrogen bonds : angle 7.10192 ( 2124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 227 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8261 (pm20) cc_final: 0.7404 (tm-30) REVERT: A 45 TYR cc_start: 0.8911 (m-80) cc_final: 0.8562 (m-80) REVERT: B 129 PHE cc_start: 0.9231 (m-10) cc_final: 0.8976 (m-10) REVERT: B 302 TYR cc_start: 0.8029 (m-80) cc_final: 0.7600 (m-10) REVERT: D 151 LEU cc_start: 0.8704 (tp) cc_final: 0.8479 (pp) REVERT: E 249 MET cc_start: 0.6096 (tpp) cc_final: 0.5316 (tpp) REVERT: E 250 MET cc_start: 0.6231 (mpp) cc_final: 0.5197 (mmt) outliers start: 11 outliers final: 4 residues processed: 232 average time/residue: 0.0769 time to fit residues: 29.1239 Evaluate side-chains 221 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 217 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.112715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083024 restraints weight = 43559.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.085354 restraints weight = 25854.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.086635 restraints weight = 17848.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.087883 restraints weight = 14320.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.088165 restraints weight = 11836.956| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12485 Z= 0.136 Angle : 0.717 14.189 17000 Z= 0.351 Chirality : 0.044 0.256 1939 Planarity : 0.005 0.063 2082 Dihedral : 5.270 46.339 1625 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.36 % Allowed : 30.08 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.21), residues: 1481 helix: 0.14 (0.17), residues: 908 sheet: -0.51 (0.50), residues: 97 loop : -2.48 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 404 TYR 0.022 0.001 TYR A 45 PHE 0.016 0.001 PHE E 328 TRP 0.014 0.001 TRP E 332 HIS 0.002 0.000 HIS E 312 Details of bonding type rmsd covalent geometry : bond 0.00294 (12474) covalent geometry : angle 0.71654 (16978) SS BOND : bond 0.00149 ( 11) SS BOND : angle 1.00389 ( 22) hydrogen bonds : bond 0.04276 ( 716) hydrogen bonds : angle 5.40016 ( 2124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 225 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8121 (pm20) cc_final: 0.7227 (tm-30) REVERT: A 86 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8844 (mm) REVERT: A 146 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8137 (ppt170) REVERT: A 187 ASP cc_start: 0.7410 (t0) cc_final: 0.7094 (t0) REVERT: B 146 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7643 (ptt-90) REVERT: B 201 PHE cc_start: 0.8891 (m-10) cc_final: 0.8488 (m-10) REVERT: B 302 TYR cc_start: 0.7940 (m-80) cc_final: 0.7576 (m-10) REVERT: C 129 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8629 (t80) REVERT: D 146 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8236 (mpp-170) REVERT: D 277 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8055 (tp30) REVERT: E 250 MET cc_start: 0.6111 (mpp) cc_final: 0.5380 (mmt) outliers start: 58 outliers final: 27 residues processed: 264 average time/residue: 0.0858 time to fit residues: 35.1101 Evaluate side-chains 236 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 264 PHE Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 301 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 122 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 HIS C 101 ASN D 140 HIS D 294 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.109602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.079535 restraints weight = 44584.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.081543 restraints weight = 26216.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.083270 restraints weight = 18580.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.084067 restraints weight = 14339.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.084491 restraints weight = 12255.224| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12485 Z= 0.165 Angle : 0.696 11.538 17000 Z= 0.345 Chirality : 0.044 0.230 1939 Planarity : 0.004 0.061 2082 Dihedral : 4.742 41.930 1619 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 7.14 % Allowed : 27.29 % Favored : 65.56 % 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: -0.59 (0.21), residues: 1481 helix: 0.65 (0.17), residues: 919 sheet: -0.69 (0.49), residues: 97 loop : -2.43 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 77 TYR 0.011 0.001 TYR D 219 PHE 0.017 0.001 PHE A 199 TRP 0.014 0.001 TRP E 332 HIS 0.002 0.001 HIS E 312 Details of bonding type rmsd covalent geometry : bond 0.00375 (12474) covalent geometry : angle 0.69589 (16978) SS BOND : bond 0.00175 ( 11) SS BOND : angle 0.81606 ( 22) hydrogen bonds : bond 0.04092 ( 716) hydrogen bonds : angle 5.05642 ( 2124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 214 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8217 (pm20) cc_final: 0.7375 (tm-30) REVERT: A 86 LEU cc_start: 0.9205 (mm) cc_final: 0.8847 (mm) REVERT: A 146 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8254 (ppt170) REVERT: A 187 ASP cc_start: 0.7980 (t0) cc_final: 0.7659 (t70) REVERT: B 146 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7723 (ptt-90) REVERT: B 201 PHE cc_start: 0.8979 (m-10) cc_final: 0.8642 (m-10) REVERT: B 302 TYR cc_start: 0.8070 (m-80) cc_final: 0.7771 (m-10) REVERT: C 101 ASN cc_start: 0.6389 (m110) cc_final: 0.5657 (t0) REVERT: C 129 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8462 (t80) REVERT: C 288 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8448 (tm-30) REVERT: D 146 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8413 (mpp-170) REVERT: D 268 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: D 277 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8130 (tp30) REVERT: E 249 MET cc_start: 0.5808 (tpp) cc_final: 0.5565 (tpp) REVERT: E 250 MET cc_start: 0.6241 (mpp) cc_final: 0.5068 (mmt) REVERT: E 434 LEU cc_start: 0.7418 (tp) cc_final: 0.6878 (tp) outliers start: 95 outliers final: 52 residues processed: 282 average time/residue: 0.0820 time to fit residues: 36.2823 Evaluate side-chains 256 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 198 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 294 HIS Chi-restraints excluded: chain D residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 114 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.111181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.081255 restraints weight = 43982.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.083334 restraints weight = 25650.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.085053 restraints weight = 18131.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.085697 restraints weight = 14000.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.085697 restraints weight = 12148.773| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12485 Z= 0.123 Angle : 0.707 12.909 17000 Z= 0.337 Chirality : 0.043 0.237 1939 Planarity : 0.004 0.061 2082 Dihedral : 4.655 40.423 1619 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.32 % Allowed : 29.25 % Favored : 64.44 % 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: -0.37 (0.22), residues: 1481 helix: 0.86 (0.17), residues: 916 sheet: -0.68 (0.51), residues: 97 loop : -2.38 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.010 0.001 TYR A 256 PHE 0.014 0.001 PHE A 199 TRP 0.013 0.001 TRP E 332 HIS 0.014 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00271 (12474) covalent geometry : angle 0.70568 (16978) SS BOND : bond 0.00145 ( 11) SS BOND : angle 1.23448 ( 22) hydrogen bonds : bond 0.03877 ( 716) hydrogen bonds : angle 4.95765 ( 2124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 223 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8251 (pm20) cc_final: 0.7429 (tm-30) REVERT: A 86 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8793 (mm) REVERT: A 146 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8166 (ppt170) REVERT: A 187 ASP cc_start: 0.7989 (t0) cc_final: 0.7783 (t0) REVERT: B 146 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7697 (ptt-90) REVERT: B 201 PHE cc_start: 0.8954 (m-10) cc_final: 0.8525 (m-10) REVERT: B 302 TYR cc_start: 0.7996 (m-80) cc_final: 0.7699 (m-10) REVERT: C 101 ASN cc_start: 0.6462 (m110) cc_final: 0.6102 (t0) REVERT: C 129 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8182 (t80) REVERT: D 268 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: D 277 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: D 293 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7998 (t80) REVERT: E 249 MET cc_start: 0.5814 (tpp) cc_final: 0.5424 (tpp) REVERT: E 250 MET cc_start: 0.6287 (mpp) cc_final: 0.5184 (mmt) REVERT: E 434 LEU cc_start: 0.7448 (tp) cc_final: 0.6910 (tp) outliers start: 84 outliers final: 48 residues processed: 283 average time/residue: 0.0800 time to fit residues: 35.7788 Evaluate side-chains 256 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 264 PHE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 383 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 148 optimal weight: 40.0000 chunk 54 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 123 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.111288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.082095 restraints weight = 44238.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.084334 restraints weight = 26047.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.085636 restraints weight = 18176.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.086902 restraints weight = 14242.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.087191 restraints weight = 11966.264| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12485 Z= 0.124 Angle : 0.705 13.198 17000 Z= 0.335 Chirality : 0.043 0.280 1939 Planarity : 0.004 0.060 2082 Dihedral : 4.561 34.383 1619 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.32 % Allowed : 29.25 % Favored : 64.44 % 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: -0.27 (0.22), residues: 1481 helix: 0.97 (0.17), residues: 910 sheet: -0.71 (0.52), residues: 97 loop : -2.38 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 77 TYR 0.010 0.001 TYR A 256 PHE 0.012 0.001 PHE E 328 TRP 0.012 0.001 TRP E 332 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00275 (12474) covalent geometry : angle 0.70453 (16978) SS BOND : bond 0.00126 ( 11) SS BOND : angle 0.83202 ( 22) hydrogen bonds : bond 0.03804 ( 716) hydrogen bonds : angle 4.89656 ( 2124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 217 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8221 (pm20) cc_final: 0.7471 (tm-30) REVERT: A 63 MET cc_start: 0.8461 (mmm) cc_final: 0.8243 (mmm) REVERT: A 86 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 146 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8093 (ppt170) REVERT: A 205 MET cc_start: 0.7927 (mpp) cc_final: 0.7717 (mtm) REVERT: B 146 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7587 (ptt-90) REVERT: B 281 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.8090 (t-90) REVERT: B 302 TYR cc_start: 0.7985 (m-80) cc_final: 0.7762 (m-10) REVERT: C 101 ASN cc_start: 0.6473 (m110) cc_final: 0.6152 (t0) REVERT: C 129 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8165 (t80) REVERT: D 268 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: D 277 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7933 (tp30) REVERT: E 249 MET cc_start: 0.5592 (tpp) cc_final: 0.5126 (tpp) REVERT: E 250 MET cc_start: 0.6242 (mpp) cc_final: 0.5132 (mmt) REVERT: E 434 LEU cc_start: 0.7488 (tp) cc_final: 0.6948 (tp) outliers start: 84 outliers final: 60 residues processed: 279 average time/residue: 0.0812 time to fit residues: 36.4719 Evaluate side-chains 270 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 203 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 281 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 264 PHE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 383 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.106853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.076500 restraints weight = 44320.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.078622 restraints weight = 26342.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.079898 restraints weight = 18570.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.080912 restraints weight = 14797.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.081712 restraints weight = 12453.956| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12485 Z= 0.210 Angle : 0.753 12.648 17000 Z= 0.372 Chirality : 0.046 0.267 1939 Planarity : 0.004 0.060 2082 Dihedral : 4.574 32.829 1619 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 7.44 % Allowed : 28.50 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1481 helix: 0.94 (0.17), residues: 912 sheet: -0.79 (0.52), residues: 97 loop : -2.34 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 77 TYR 0.016 0.002 TYR A 103 PHE 0.017 0.002 PHE E 328 TRP 0.016 0.001 TRP E 332 HIS 0.004 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00480 (12474) covalent geometry : angle 0.75304 (16978) SS BOND : bond 0.00199 ( 11) SS BOND : angle 0.88925 ( 22) hydrogen bonds : bond 0.04135 ( 716) hydrogen bonds : angle 5.06442 ( 2124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 213 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8230 (pm20) cc_final: 0.7405 (tm-30) REVERT: A 32 GLU cc_start: 0.5262 (OUTLIER) cc_final: 0.5037 (tp30) REVERT: A 63 MET cc_start: 0.8650 (mmm) cc_final: 0.8415 (mmm) REVERT: A 86 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8887 (mm) REVERT: A 256 TYR cc_start: 0.8600 (m-80) cc_final: 0.8357 (m-10) REVERT: B 146 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7671 (ptt-90) REVERT: B 223 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9131 (tp) REVERT: B 281 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.8263 (t-90) REVERT: C 101 ASN cc_start: 0.6649 (m110) cc_final: 0.6326 (m-40) REVERT: C 129 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8521 (t80) REVERT: C 172 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8681 (m-10) REVERT: C 230 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6799 (pptt) REVERT: D 108 LEU cc_start: 0.9200 (mp) cc_final: 0.8997 (mt) REVERT: D 268 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: D 277 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8028 (tp30) REVERT: E 249 MET cc_start: 0.5739 (tpp) cc_final: 0.5209 (tpp) REVERT: E 250 MET cc_start: 0.6182 (mpp) cc_final: 0.5095 (mmt) REVERT: E 434 LEU cc_start: 0.7410 (tp) cc_final: 0.6871 (tp) outliers start: 99 outliers final: 73 residues processed: 290 average time/residue: 0.0778 time to fit residues: 36.5397 Evaluate side-chains 284 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 201 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 281 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 294 HIS Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 383 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 12 optimal weight: 0.0170 chunk 24 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 70 optimal weight: 0.0470 chunk 146 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.109223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.080508 restraints weight = 44141.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.082731 restraints weight = 25780.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083963 restraints weight = 17943.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.085189 restraints weight = 14091.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.085508 restraints weight = 11863.886| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12485 Z= 0.130 Angle : 0.731 13.244 17000 Z= 0.351 Chirality : 0.044 0.253 1939 Planarity : 0.004 0.057 2082 Dihedral : 4.517 33.316 1619 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.02 % Allowed : 30.90 % Favored : 63.08 % 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: -0.19 (0.22), residues: 1481 helix: 1.03 (0.17), residues: 910 sheet: -0.75 (0.52), residues: 97 loop : -2.32 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 77 TYR 0.011 0.001 TYR A 256 PHE 0.020 0.001 PHE C 87 TRP 0.013 0.001 TRP E 332 HIS 0.005 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00290 (12474) covalent geometry : angle 0.73093 (16978) SS BOND : bond 0.00160 ( 11) SS BOND : angle 1.01738 ( 22) hydrogen bonds : bond 0.03955 ( 716) hydrogen bonds : angle 4.94382 ( 2124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 222 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8199 (pm20) cc_final: 0.7473 (tm-30) REVERT: A 32 GLU cc_start: 0.5238 (OUTLIER) cc_final: 0.5024 (tp30) REVERT: A 63 MET cc_start: 0.8416 (mmm) cc_final: 0.8209 (mmm) REVERT: A 86 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8826 (mm) REVERT: B 146 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7592 (ptt-90) REVERT: B 281 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8031 (t-90) REVERT: B 302 TYR cc_start: 0.8175 (m-10) cc_final: 0.7949 (m-10) REVERT: C 101 ASN cc_start: 0.6678 (m110) cc_final: 0.6360 (t0) REVERT: C 129 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8394 (t80) REVERT: C 230 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6787 (pptt) REVERT: D 108 LEU cc_start: 0.9102 (mp) cc_final: 0.8888 (mt) REVERT: E 249 MET cc_start: 0.5529 (tpp) cc_final: 0.4961 (tpp) REVERT: E 250 MET cc_start: 0.6156 (mpp) cc_final: 0.5087 (mmt) REVERT: E 434 LEU cc_start: 0.7447 (tp) cc_final: 0.6883 (tp) outliers start: 80 outliers final: 60 residues processed: 278 average time/residue: 0.0745 time to fit residues: 33.4063 Evaluate side-chains 277 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 211 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 281 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 383 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 118 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 117 optimal weight: 30.0000 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.110514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.081016 restraints weight = 44368.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.083272 restraints weight = 25714.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.084377 restraints weight = 17842.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.085772 restraints weight = 14300.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.086153 restraints weight = 11966.276| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12485 Z= 0.130 Angle : 0.734 13.506 17000 Z= 0.351 Chirality : 0.045 0.268 1939 Planarity : 0.004 0.055 2082 Dihedral : 4.355 23.928 1617 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.71 % Allowed : 31.50 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1481 helix: 1.04 (0.17), residues: 910 sheet: -0.60 (0.52), residues: 97 loop : -2.31 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 77 TYR 0.010 0.001 TYR A 256 PHE 0.020 0.001 PHE C 87 TRP 0.015 0.001 TRP C 195 HIS 0.003 0.000 HIS C 294 Details of bonding type rmsd covalent geometry : bond 0.00296 (12474) covalent geometry : angle 0.73399 (16978) SS BOND : bond 0.00133 ( 11) SS BOND : angle 0.88044 ( 22) hydrogen bonds : bond 0.03912 ( 716) hydrogen bonds : angle 4.91665 ( 2124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 221 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8287 (pm20) cc_final: 0.7521 (tm-30) REVERT: A 45 TYR cc_start: 0.8905 (m-80) cc_final: 0.8526 (m-80) REVERT: A 63 MET cc_start: 0.8506 (mmm) cc_final: 0.8292 (mmm) REVERT: A 86 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8805 (mm) REVERT: B 31 GLU cc_start: 0.7745 (mp0) cc_final: 0.7439 (mp0) REVERT: B 146 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7639 (ptt-90) REVERT: B 281 HIS cc_start: 0.8552 (OUTLIER) cc_final: 0.8159 (t-90) REVERT: B 302 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7945 (m-10) REVERT: C 101 ASN cc_start: 0.6669 (m110) cc_final: 0.6339 (t0) REVERT: C 129 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8440 (t80) REVERT: D 108 LEU cc_start: 0.9106 (mp) cc_final: 0.8885 (mt) REVERT: D 205 MET cc_start: 0.7470 (mtt) cc_final: 0.7270 (mtm) REVERT: D 268 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: E 249 MET cc_start: 0.5693 (tpp) cc_final: 0.4311 (tpp) REVERT: E 250 MET cc_start: 0.6260 (mpp) cc_final: 0.5197 (mmt) REVERT: E 434 LEU cc_start: 0.7448 (tp) cc_final: 0.6884 (tp) outliers start: 76 outliers final: 60 residues processed: 274 average time/residue: 0.0777 time to fit residues: 34.0018 Evaluate side-chains 275 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 209 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 281 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 383 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 108 optimal weight: 0.0570 chunk 70 optimal weight: 0.7980 chunk 117 optimal weight: 50.0000 chunk 51 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 115 optimal weight: 20.0000 chunk 97 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.110394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.082094 restraints weight = 44384.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.084360 restraints weight = 25944.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.085866 restraints weight = 17930.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.086577 restraints weight = 13899.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.087196 restraints weight = 11902.351| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12485 Z= 0.129 Angle : 0.756 14.494 17000 Z= 0.359 Chirality : 0.045 0.291 1939 Planarity : 0.004 0.056 2082 Dihedral : 4.314 24.142 1617 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.11 % Allowed : 31.95 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1481 helix: 1.02 (0.17), residues: 910 sheet: -0.49 (0.52), residues: 97 loop : -2.29 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.011 0.001 TYR A 256 PHE 0.017 0.001 PHE C 87 TRP 0.012 0.001 TRP E 332 HIS 0.003 0.000 HIS C 294 Details of bonding type rmsd covalent geometry : bond 0.00289 (12474) covalent geometry : angle 0.75596 (16978) SS BOND : bond 0.00131 ( 11) SS BOND : angle 0.80704 ( 22) hydrogen bonds : bond 0.03876 ( 716) hydrogen bonds : angle 4.88929 ( 2124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8262 (pm20) cc_final: 0.7405 (tm-30) REVERT: A 63 MET cc_start: 0.8387 (mmm) cc_final: 0.8158 (mmm) REVERT: A 86 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8782 (mm) REVERT: A 187 ASP cc_start: 0.6964 (t0) cc_final: 0.6721 (t0) REVERT: B 31 GLU cc_start: 0.7762 (mp0) cc_final: 0.7489 (mp0) REVERT: B 146 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7568 (ptt-90) REVERT: B 244 LEU cc_start: 0.9054 (tp) cc_final: 0.8754 (tt) REVERT: B 274 CYS cc_start: 0.7690 (m) cc_final: 0.7217 (t) REVERT: B 281 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8039 (t-90) REVERT: B 302 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7899 (m-10) REVERT: C 101 ASN cc_start: 0.6787 (m110) cc_final: 0.6493 (t0) REVERT: C 129 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8429 (t80) REVERT: D 108 LEU cc_start: 0.9067 (mp) cc_final: 0.8855 (mt) REVERT: D 268 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: E 249 MET cc_start: 0.5523 (tpp) cc_final: 0.4132 (tpp) REVERT: E 250 MET cc_start: 0.6156 (mpp) cc_final: 0.5109 (mmt) REVERT: E 434 LEU cc_start: 0.7470 (tp) cc_final: 0.6894 (tp) outliers start: 68 outliers final: 53 residues processed: 267 average time/residue: 0.0800 time to fit residues: 34.1020 Evaluate side-chains 270 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 281 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 383 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.109144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.079717 restraints weight = 44534.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.081947 restraints weight = 25915.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.083215 restraints weight = 17974.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.084446 restraints weight = 14117.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.084888 restraints weight = 11976.171| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12485 Z= 0.158 Angle : 0.769 14.478 17000 Z= 0.370 Chirality : 0.046 0.280 1939 Planarity : 0.004 0.056 2082 Dihedral : 4.297 21.506 1617 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 5.71 % Allowed : 31.73 % Favored : 62.56 % 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: -0.13 (0.22), residues: 1481 helix: 1.03 (0.17), residues: 910 sheet: -0.51 (0.52), residues: 97 loop : -2.23 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.012 0.001 TYR A 103 PHE 0.016 0.001 PHE E 328 TRP 0.014 0.001 TRP E 332 HIS 0.004 0.001 HIS E 410 Details of bonding type rmsd covalent geometry : bond 0.00374 (12474) covalent geometry : angle 0.76830 (16978) SS BOND : bond 0.00185 ( 11) SS BOND : angle 0.93910 ( 22) hydrogen bonds : bond 0.04012 ( 716) hydrogen bonds : angle 4.94022 ( 2124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 211 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8273 (pm20) cc_final: 0.7457 (tm-30) REVERT: A 45 TYR cc_start: 0.8946 (m-80) cc_final: 0.8658 (m-80) REVERT: A 63 MET cc_start: 0.8550 (mmm) cc_final: 0.8302 (mmm) REVERT: A 86 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8834 (mm) REVERT: A 187 ASP cc_start: 0.7048 (t0) cc_final: 0.6772 (t0) REVERT: A 256 TYR cc_start: 0.8602 (m-80) cc_final: 0.8275 (m-10) REVERT: B 31 GLU cc_start: 0.7801 (mp0) cc_final: 0.7524 (mp0) REVERT: B 146 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7625 (ptt-90) REVERT: B 223 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8976 (tp) REVERT: B 274 CYS cc_start: 0.7755 (m) cc_final: 0.7279 (t) REVERT: B 281 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.8215 (t-90) REVERT: C 101 ASN cc_start: 0.6723 (m110) cc_final: 0.6464 (m-40) REVERT: C 129 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8569 (t80) REVERT: C 209 ILE cc_start: 0.9138 (pt) cc_final: 0.8629 (tp) REVERT: D 268 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: E 249 MET cc_start: 0.5698 (tpp) cc_final: 0.4320 (tpp) REVERT: E 250 MET cc_start: 0.6273 (mpp) cc_final: 0.5245 (mmt) REVERT: E 434 LEU cc_start: 0.7372 (tp) cc_final: 0.6806 (tp) outliers start: 76 outliers final: 59 residues processed: 265 average time/residue: 0.0792 time to fit residues: 33.6457 Evaluate side-chains 271 residues out of total 1330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 281 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 294 HIS Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 383 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 104 optimal weight: 6.9990 chunk 129 optimal weight: 40.0000 chunk 93 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 121 optimal weight: 0.0370 chunk 110 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** 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 = 0.4013 r_free = 0.4013 target = 0.109874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.081182 restraints weight = 44075.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.083436 restraints weight = 25270.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.085040 restraints weight = 17402.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.085745 restraints weight = 13365.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.086388 restraints weight = 11464.020| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12485 Z= 0.133 Angle : 0.770 14.623 17000 Z= 0.368 Chirality : 0.046 0.268 1939 Planarity : 0.004 0.056 2082 Dihedral : 4.330 22.118 1617 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.96 % Allowed : 32.48 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1481 helix: 0.99 (0.17), residues: 910 sheet: -0.42 (0.52), residues: 97 loop : -2.23 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.011 0.001 TYR A 256 PHE 0.016 0.001 PHE E 328 TRP 0.013 0.001 TRP E 332 HIS 0.007 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00305 (12474) covalent geometry : angle 0.76987 (16978) SS BOND : bond 0.00149 ( 11) SS BOND : angle 0.87181 ( 22) hydrogen bonds : bond 0.03953 ( 716) hydrogen bonds : angle 4.92583 ( 2124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2044.33 seconds wall clock time: 36 minutes 21.54 seconds (2181.54 seconds total)