Starting phenix.real_space_refine on Tue Mar 3 23:15:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y35_33588/03_2026/7y35_33588.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y35_33588/03_2026/7y35_33588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y35_33588/03_2026/7y35_33588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y35_33588/03_2026/7y35_33588.map" model { file = "/net/cci-nas-00/data/ceres_data/7y35_33588/03_2026/7y35_33588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y35_33588/03_2026/7y35_33588.cif" } resolution = 2.9 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= 0.003 sd= 0.038 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 56 5.16 5 C 5841 2.51 5 N 1616 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9191 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3053 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 3 Chain: "P" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 273 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1858 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 1.79, per 1000 atoms: 0.19 Number of scatterers: 9191 At special positions: 0 Unit cell: (127.764, 98.358, 151.086, 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 56 16.00 O 1678 8.00 N 1616 7.00 C 5841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.05 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 370.5 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 41.5% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'R' and resid 33 through 57 Processing helix chain 'R' and resid 167 through 172 removed outlier: 3.620A pdb=" N VAL R 171 " --> pdb=" O TYR R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 212 removed outlier: 4.347A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 244 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.745A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.507A pdb=" N TRP R 329 " --> pdb=" O THR R 325 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 414 Processing helix chain 'R' and resid 420 through 424 removed outlier: 3.590A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.568A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 removed outlier: 3.749A pdb=" N LEU R 481 " --> pdb=" O TRP R 477 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 33 removed outlier: 4.097A pdb=" N LYS P 30 " --> pdb=" O LYS P 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.913A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.658A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.884A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.642A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.980A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.665A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.510A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.873A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.793A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.713A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.520A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 111 through 112 Processing sheet with id=AA2, first strand: chain 'R' and resid 126 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.655A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.531A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.803A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.956A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.531A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.739A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.551A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.674A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.653A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1344 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: 1.69 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1492 1.31 - 1.44: 2658 1.44 - 1.57: 5161 1.57 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 9389 Sorted by residual: bond pdb=" CA PHE R 173 " pdb=" C PHE R 173 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.32e-02 5.74e+03 2.10e+01 bond pdb=" C GLU R 180 " pdb=" O GLU R 180 " ideal model delta sigma weight residual 1.236 1.182 0.055 1.47e-02 4.63e+03 1.38e+01 bond pdb=" N GLU R 177 " pdb=" CA GLU R 177 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.30e+01 bond pdb=" CA GLU R 177 " pdb=" C GLU R 177 " ideal model delta sigma weight residual 1.523 1.566 -0.043 1.34e-02 5.57e+03 1.03e+01 bond pdb=" N THR R 175 " pdb=" CA THR R 175 " ideal model delta sigma weight residual 1.457 1.423 0.035 1.29e-02 6.01e+03 7.27e+00 ... (remaining 9384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 12632 3.45 - 6.90: 68 6.90 - 10.35: 5 10.35 - 13.79: 1 13.79 - 17.24: 2 Bond angle restraints: 12708 Sorted by residual: angle pdb=" CA LYS R 172 " pdb=" C LYS R 172 " pdb=" N PHE R 173 " ideal model delta sigma weight residual 117.63 100.39 17.24 1.25e+00 6.40e-01 1.90e+02 angle pdb=" C LYS R 172 " pdb=" N PHE R 173 " pdb=" CA PHE R 173 " ideal model delta sigma weight residual 120.54 136.29 -15.75 1.35e+00 5.49e-01 1.36e+02 angle pdb=" O LYS R 172 " pdb=" C LYS R 172 " pdb=" N PHE R 173 " ideal model delta sigma weight residual 122.22 133.17 -10.95 1.17e+00 7.31e-01 8.75e+01 angle pdb=" N ASN R 176 " pdb=" CA ASN R 176 " pdb=" C ASN R 176 " ideal model delta sigma weight residual 112.23 120.32 -8.09 1.26e+00 6.30e-01 4.12e+01 angle pdb=" C ASN R 176 " pdb=" N GLU R 177 " pdb=" CA GLU R 177 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 ... (remaining 12703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 5084 16.82 - 33.64: 391 33.64 - 50.46: 77 50.46 - 67.28: 11 67.28 - 84.11: 11 Dihedral angle restraints: 5574 sinusoidal: 2231 harmonic: 3343 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -9.29 -76.71 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 5571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 846 0.040 - 0.081: 380 0.081 - 0.121: 145 0.121 - 0.162: 30 0.162 - 0.202: 4 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA PHE R 335 " pdb=" N PHE R 335 " pdb=" C PHE R 335 " pdb=" CB PHE R 335 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA TYR R 191 " pdb=" N TYR R 191 " pdb=" C TYR R 191 " pdb=" CB TYR R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA VAL R 157 " pdb=" N VAL R 157 " pdb=" C VAL R 157 " pdb=" CB VAL R 157 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 1402 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS R 172 " 0.032 2.00e-02 2.50e+03 7.65e-02 5.85e+01 pdb=" C LYS R 172 " -0.132 2.00e-02 2.50e+03 pdb=" O LYS R 172 " 0.056 2.00e-02 2.50e+03 pdb=" N PHE R 173 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO B 236 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 175 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C THR R 175 " -0.042 2.00e-02 2.50e+03 pdb=" O THR R 175 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN R 176 " 0.014 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1441 2.75 - 3.29: 8451 3.29 - 3.83: 15173 3.83 - 4.36: 18199 4.36 - 4.90: 31860 Nonbonded interactions: 75124 Sorted by model distance: nonbonded pdb=" ND2 ASN R 448 " pdb=" OE2 GLU P 4 " model vdw 2.217 3.120 nonbonded pdb=" NH1 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.226 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.264 3.040 nonbonded pdb=" OE2 GLU A 27 " pdb=" NZ LYS B 89 " model vdw 2.306 3.120 nonbonded pdb=" NE1 TRP R 437 " pdb=" OD2 ASP P 10 " model vdw 2.341 3.120 ... (remaining 75119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.040 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.009 0.104 9396 Z= 0.426 Angle : 0.802 17.243 12720 Z= 0.480 Chirality : 0.052 0.202 1405 Planarity : 0.005 0.076 1617 Dihedral : 12.994 84.106 3394 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.95 % 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: -1.37 (0.23), residues: 1123 helix: -0.13 (0.23), residues: 440 sheet: -1.02 (0.30), residues: 258 loop : -1.51 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 400 TYR 0.042 0.002 TYR B 59 PHE 0.022 0.002 PHE R 335 TRP 0.027 0.003 TRP B 99 HIS 0.016 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00903 ( 9389) covalent geometry : angle 0.79509 (12708) SS BOND : bond 0.00937 ( 6) SS BOND : angle 3.49735 ( 12) hydrogen bonds : bond 0.17052 ( 464) hydrogen bonds : angle 6.54788 ( 1344) Misc. bond : bond 0.10398 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8777 (mp0) cc_final: 0.8368 (mp0) REVERT: R 36 GLU cc_start: 0.8431 (tp30) cc_final: 0.7973 (tp30) REVERT: R 37 GLN cc_start: 0.8764 (tp40) cc_final: 0.8237 (tp-100) REVERT: R 45 GLN cc_start: 0.8892 (tt0) cc_final: 0.8514 (tt0) REVERT: R 47 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8624 (mm110) REVERT: R 137 ASP cc_start: 0.8025 (m-30) cc_final: 0.7727 (m-30) REVERT: R 149 ASP cc_start: 0.7503 (t70) cc_final: 0.7221 (t0) REVERT: R 156 LEU cc_start: 0.7207 (mt) cc_final: 0.6890 (tt) REVERT: R 160 HIS cc_start: 0.7424 (m90) cc_final: 0.6797 (m90) REVERT: R 407 LEU cc_start: 0.8372 (tp) cc_final: 0.8170 (tt) REVERT: P 18 LEU cc_start: 0.9086 (tp) cc_final: 0.8617 (tm) REVERT: P 19 ARG cc_start: 0.8945 (mtp180) cc_final: 0.8688 (mtm180) REVERT: P 22 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 17 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7857 (mmtm) REVERT: A 27 GLU cc_start: 0.7022 (mp0) cc_final: 0.6816 (mp0) REVERT: A 34 LYS cc_start: 0.8928 (tttt) cc_final: 0.8518 (ttpp) REVERT: A 38 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7477 (mtm110) REVERT: A 311 TYR cc_start: 0.8140 (m-80) cc_final: 0.7845 (m-80) REVERT: A 344 GLU cc_start: 0.7881 (tp30) cc_final: 0.7530 (tp30) REVERT: A 378 ASP cc_start: 0.8003 (m-30) cc_final: 0.7755 (m-30) REVERT: B 22 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7199 (mtm180) REVERT: B 25 CYS cc_start: 0.8133 (m) cc_final: 0.7273 (p) REVERT: B 52 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8292 (mtt-85) REVERT: B 66 ASP cc_start: 0.7511 (p0) cc_final: 0.7270 (p0) REVERT: B 215 GLU cc_start: 0.7835 (mp0) cc_final: 0.7544 (mp0) REVERT: B 246 ASP cc_start: 0.7945 (m-30) cc_final: 0.6938 (m-30) REVERT: B 254 ASP cc_start: 0.7917 (m-30) cc_final: 0.7690 (m-30) REVERT: B 258 ASP cc_start: 0.7908 (t0) cc_final: 0.6961 (t0) REVERT: B 267 ASP cc_start: 0.7648 (p0) cc_final: 0.7319 (p0) REVERT: B 312 ASP cc_start: 0.7262 (p0) cc_final: 0.6330 (p0) REVERT: N 35 ASN cc_start: 0.8318 (m-40) cc_final: 0.8083 (m-40) REVERT: N 69 THR cc_start: 0.8574 (m) cc_final: 0.7969 (p) REVERT: N 78 THR cc_start: 0.8495 (t) cc_final: 0.8058 (p) REVERT: N 83 MET cc_start: 0.8287 (mtp) cc_final: 0.8013 (mtm) REVERT: N 123 GLN cc_start: 0.8670 (tp40) cc_final: 0.8385 (tm-30) REVERT: N 125 THR cc_start: 0.8250 (p) cc_final: 0.7519 (p) outliers start: 1 outliers final: 0 residues processed: 345 average time/residue: 0.7444 time to fit residues: 269.4837 Evaluate side-chains 288 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 358 ASN R 364 GLN R 402 GLN R 420 HIS R 440 GLN R 463 ASN A 213 GLN A 236 GLN A 384 GLN B 13 GLN B 32 GLN B 75 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.105646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089738 restraints weight = 18138.065| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.68 r_work: 0.3197 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9396 Z= 0.154 Angle : 0.613 7.479 12720 Z= 0.326 Chirality : 0.044 0.238 1405 Planarity : 0.005 0.059 1617 Dihedral : 4.984 53.193 1260 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.55 % Allowed : 16.11 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1123 helix: 1.08 (0.25), residues: 455 sheet: -0.16 (0.33), residues: 229 loop : -1.32 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 342 TYR 0.027 0.001 TYR R 191 PHE 0.020 0.002 PHE R 314 TRP 0.025 0.002 TRP R 352 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9389) covalent geometry : angle 0.61099 (12708) SS BOND : bond 0.00567 ( 6) SS BOND : angle 1.81562 ( 12) hydrogen bonds : bond 0.05200 ( 464) hydrogen bonds : angle 4.63788 ( 1344) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 GLN cc_start: 0.8785 (tp40) cc_final: 0.8443 (tp40) REVERT: R 39 PHE cc_start: 0.8994 (t80) cc_final: 0.8634 (t80) REVERT: R 137 ASP cc_start: 0.7679 (m-30) cc_final: 0.7476 (m-30) REVERT: R 156 LEU cc_start: 0.7317 (mt) cc_final: 0.6734 (tt) REVERT: R 160 HIS cc_start: 0.7419 (m90) cc_final: 0.7035 (m90) REVERT: R 182 GLU cc_start: 0.7406 (tp30) cc_final: 0.7030 (tp30) REVERT: R 207 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8377 (mm) REVERT: R 281 CYS cc_start: 0.6154 (m) cc_final: 0.5805 (t) REVERT: R 346 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8625 (mt) REVERT: R 407 LEU cc_start: 0.8309 (tp) cc_final: 0.8004 (tt) REVERT: R 425 MET cc_start: 0.8673 (ptm) cc_final: 0.8232 (ptm) REVERT: P 21 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8133 (ttm-80) REVERT: P 27 LEU cc_start: 0.8822 (mm) cc_final: 0.8579 (mm) REVERT: A 17 LYS cc_start: 0.8280 (mmtm) cc_final: 0.7998 (mmtm) REVERT: A 27 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: A 34 LYS cc_start: 0.8990 (tttt) cc_final: 0.8640 (ttmm) REVERT: A 38 ARG cc_start: 0.8308 (mtm110) cc_final: 0.8034 (mtm110) REVERT: A 46 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8156 (tt) REVERT: A 53 LYS cc_start: 0.8424 (ttpp) cc_final: 0.8182 (ttpp) REVERT: A 54 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8810 (t) REVERT: A 240 ASP cc_start: 0.7636 (m-30) cc_final: 0.7396 (m-30) REVERT: A 311 TYR cc_start: 0.8402 (m-80) cc_final: 0.8097 (m-80) REVERT: A 380 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7949 (ttp80) REVERT: B 5 ASP cc_start: 0.7866 (p0) cc_final: 0.7375 (p0) REVERT: B 12 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7888 (pp20) REVERT: B 22 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7543 (mtm-85) REVERT: B 25 CYS cc_start: 0.8418 (m) cc_final: 0.7905 (p) REVERT: B 32 GLN cc_start: 0.8407 (mt0) cc_final: 0.8071 (mt0) REVERT: B 46 ARG cc_start: 0.8487 (mtp180) cc_final: 0.7990 (ttm110) REVERT: B 75 GLN cc_start: 0.8701 (mt0) cc_final: 0.8413 (mt0) REVERT: B 89 LYS cc_start: 0.8803 (mttp) cc_final: 0.8396 (mttp) REVERT: B 134 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7623 (mtm-85) REVERT: B 214 ARG cc_start: 0.8118 (ptp90) cc_final: 0.7641 (ptp90) REVERT: B 215 GLU cc_start: 0.8296 (mp0) cc_final: 0.7973 (mp0) REVERT: B 217 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7599 (tmm) REVERT: B 219 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8097 (mmt90) REVERT: B 246 ASP cc_start: 0.8153 (m-30) cc_final: 0.7817 (m-30) REVERT: B 254 ASP cc_start: 0.8042 (m-30) cc_final: 0.7616 (p0) REVERT: B 258 ASP cc_start: 0.8294 (t0) cc_final: 0.7013 (t0) REVERT: B 259 GLN cc_start: 0.8288 (mt0) cc_final: 0.6783 (mt0) REVERT: B 294 CYS cc_start: 0.8567 (m) cc_final: 0.8314 (t) REVERT: G 42 GLU cc_start: 0.8484 (tt0) cc_final: 0.8264 (tt0) REVERT: G 58 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8028 (mm-30) REVERT: N 34 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.9052 (mmm) REVERT: N 69 THR cc_start: 0.8838 (m) cc_final: 0.8466 (p) REVERT: N 78 THR cc_start: 0.9077 (t) cc_final: 0.8782 (p) outliers start: 35 outliers final: 15 residues processed: 310 average time/residue: 0.6208 time to fit residues: 202.6549 Evaluate side-chains 305 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 404 ARG Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN P 5 HIS P 32 HIS A 236 GLN A 357 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.100830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.085066 restraints weight = 18173.771| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.66 r_work: 0.3111 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9396 Z= 0.242 Angle : 0.648 8.201 12720 Z= 0.343 Chirality : 0.046 0.228 1405 Planarity : 0.005 0.058 1617 Dihedral : 4.907 47.809 1260 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.78 % Allowed : 18.14 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1123 helix: 1.45 (0.25), residues: 455 sheet: -0.16 (0.33), residues: 252 loop : -0.96 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 150 TYR 0.025 0.002 TYR R 191 PHE 0.017 0.002 PHE R 314 TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 9389) covalent geometry : angle 0.64693 (12708) SS BOND : bond 0.00267 ( 6) SS BOND : angle 1.47757 ( 12) hydrogen bonds : bond 0.05724 ( 464) hydrogen bonds : angle 4.61875 ( 1344) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 281 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8454 (tp30) cc_final: 0.7870 (tp30) REVERT: R 37 GLN cc_start: 0.8879 (tp40) cc_final: 0.8404 (tp-100) REVERT: R 39 PHE cc_start: 0.9058 (t80) cc_final: 0.8752 (t80) REVERT: R 40 LEU cc_start: 0.9369 (mm) cc_final: 0.8681 (mt) REVERT: R 43 ARG cc_start: 0.8464 (mmm160) cc_final: 0.8202 (mmm160) REVERT: R 137 ASP cc_start: 0.7766 (m-30) cc_final: 0.7478 (m-30) REVERT: R 156 LEU cc_start: 0.7272 (mt) cc_final: 0.6610 (tt) REVERT: R 182 GLU cc_start: 0.7641 (tp30) cc_final: 0.7228 (tp30) REVERT: R 207 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8399 (mm) REVERT: R 213 ARG cc_start: 0.8001 (tpt-90) cc_final: 0.7759 (tpt-90) REVERT: R 346 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8707 (mt) REVERT: R 364 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8419 (mm-40) REVERT: R 407 LEU cc_start: 0.8372 (tp) cc_final: 0.8086 (tt) REVERT: R 425 MET cc_start: 0.8769 (ptm) cc_final: 0.8403 (ptm) REVERT: P 21 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8230 (ttm-80) REVERT: P 27 LEU cc_start: 0.8851 (mm) cc_final: 0.8511 (mm) REVERT: A 17 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8204 (mmtm) REVERT: A 27 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 34 LYS cc_start: 0.9014 (tttt) cc_final: 0.8770 (ttmm) REVERT: A 38 ARG cc_start: 0.8329 (mtm110) cc_final: 0.8073 (mtm110) REVERT: A 46 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8273 (tt) REVERT: A 53 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8248 (ttmm) REVERT: A 215 ASP cc_start: 0.7546 (m-30) cc_final: 0.7258 (t70) REVERT: A 311 TYR cc_start: 0.8392 (m-80) cc_final: 0.8084 (m-80) REVERT: B 5 ASP cc_start: 0.8137 (p0) cc_final: 0.7860 (p0) REVERT: B 19 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8325 (ttp80) REVERT: B 22 ARG cc_start: 0.8383 (mtt180) cc_final: 0.7789 (mtm180) REVERT: B 25 CYS cc_start: 0.8428 (m) cc_final: 0.7998 (p) REVERT: B 32 GLN cc_start: 0.8435 (mt0) cc_final: 0.8090 (mt0) REVERT: B 89 LYS cc_start: 0.8794 (mttp) cc_final: 0.8461 (mttp) REVERT: B 214 ARG cc_start: 0.8015 (ptp90) cc_final: 0.7550 (ptp90) REVERT: B 215 GLU cc_start: 0.8352 (mp0) cc_final: 0.8067 (mp0) REVERT: B 217 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7874 (tmm) REVERT: B 219 ARG cc_start: 0.8417 (tpp80) cc_final: 0.8169 (mmt90) REVERT: B 234 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: B 246 ASP cc_start: 0.8104 (m-30) cc_final: 0.7830 (m-30) REVERT: B 258 ASP cc_start: 0.8295 (t0) cc_final: 0.7440 (t0) REVERT: B 259 GLN cc_start: 0.8439 (mt0) cc_final: 0.7175 (mt0) REVERT: B 294 CYS cc_start: 0.8487 (m) cc_final: 0.8261 (t) REVERT: N 25 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8300 (p) REVERT: N 34 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8974 (mmm) REVERT: N 69 THR cc_start: 0.8962 (m) cc_final: 0.8654 (p) outliers start: 57 outliers final: 26 residues processed: 305 average time/residue: 0.7362 time to fit residues: 235.9992 Evaluate side-chains 314 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 279 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 364 GLN Chi-restraints excluded: chain R residue 404 ARG Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 0.0050 chunk 41 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 5 HIS A 357 HIS A 384 GLN B 75 GLN N 31 ASN N 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.101195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.085048 restraints weight = 18185.796| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.70 r_work: 0.3105 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9396 Z= 0.206 Angle : 0.629 9.047 12720 Z= 0.332 Chirality : 0.045 0.202 1405 Planarity : 0.004 0.056 1617 Dihedral : 4.785 49.124 1260 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.67 % Allowed : 19.05 % Favored : 75.28 % 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: 0.64 (0.26), residues: 1123 helix: 1.72 (0.25), residues: 449 sheet: 0.11 (0.34), residues: 243 loop : -0.73 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 333 TYR 0.025 0.001 TYR R 191 PHE 0.014 0.002 PHE B 151 TRP 0.021 0.002 TRP R 164 HIS 0.004 0.001 HIS R 114 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9389) covalent geometry : angle 0.62760 (12708) SS BOND : bond 0.00260 ( 6) SS BOND : angle 1.28604 ( 12) hydrogen bonds : bond 0.05240 ( 464) hydrogen bonds : angle 4.44012 ( 1344) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 286 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8419 (tp30) cc_final: 0.7891 (tp30) REVERT: R 37 GLN cc_start: 0.8875 (tp40) cc_final: 0.8451 (tp-100) REVERT: R 39 PHE cc_start: 0.9011 (t80) cc_final: 0.8695 (t80) REVERT: R 40 LEU cc_start: 0.9348 (mm) cc_final: 0.9072 (tp) REVERT: R 137 ASP cc_start: 0.7860 (m-30) cc_final: 0.7590 (m-30) REVERT: R 154 TRP cc_start: 0.6945 (m100) cc_final: 0.6734 (m100) REVERT: R 156 LEU cc_start: 0.7463 (mt) cc_final: 0.6731 (tt) REVERT: R 182 GLU cc_start: 0.7694 (tp30) cc_final: 0.7281 (tp30) REVERT: R 207 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8383 (mm) REVERT: R 213 ARG cc_start: 0.7968 (tpt-90) cc_final: 0.7728 (tpt-90) REVERT: R 346 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8695 (mt) REVERT: R 407 LEU cc_start: 0.8366 (tp) cc_final: 0.8107 (tt) REVERT: R 425 MET cc_start: 0.8776 (ptm) cc_final: 0.8403 (ptm) REVERT: R 431 GLU cc_start: 0.7630 (tp30) cc_final: 0.7416 (tp30) REVERT: R 469 GLU cc_start: 0.8198 (tp30) cc_final: 0.7655 (tp30) REVERT: P 21 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8291 (ttm-80) REVERT: A 17 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8190 (mmtm) REVERT: A 27 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 29 GLN cc_start: 0.8424 (tp-100) cc_final: 0.7916 (tm-30) REVERT: A 38 ARG cc_start: 0.8368 (mtm110) cc_final: 0.8143 (mtm110) REVERT: A 46 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 53 LYS cc_start: 0.8460 (ttpp) cc_final: 0.8258 (ttmm) REVERT: A 54 SER cc_start: 0.9295 (OUTLIER) cc_final: 0.8813 (p) REVERT: A 347 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8075 (ttm-80) REVERT: A 381 ASP cc_start: 0.8560 (t0) cc_final: 0.8315 (t0) REVERT: B 12 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7985 (pp20) REVERT: B 13 GLN cc_start: 0.8838 (mm110) cc_final: 0.8612 (mm-40) REVERT: B 22 ARG cc_start: 0.8466 (mtt180) cc_final: 0.7930 (mtm180) REVERT: B 25 CYS cc_start: 0.8513 (m) cc_final: 0.8025 (p) REVERT: B 32 GLN cc_start: 0.8431 (mt0) cc_final: 0.8099 (mt0) REVERT: B 59 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: B 75 GLN cc_start: 0.8613 (mt0) cc_final: 0.8345 (mt0) REVERT: B 89 LYS cc_start: 0.8792 (mttp) cc_final: 0.8491 (mttp) REVERT: B 214 ARG cc_start: 0.8064 (ptp90) cc_final: 0.7577 (ptp90) REVERT: B 215 GLU cc_start: 0.8368 (mp0) cc_final: 0.8148 (mp0) REVERT: B 217 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7851 (tmm) REVERT: B 219 ARG cc_start: 0.8387 (tpp80) cc_final: 0.7948 (mtt90) REVERT: B 234 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: B 246 ASP cc_start: 0.8095 (m-30) cc_final: 0.7804 (m-30) REVERT: B 258 ASP cc_start: 0.8255 (t0) cc_final: 0.7392 (t0) REVERT: B 259 GLN cc_start: 0.8462 (mt0) cc_final: 0.7290 (mt0) REVERT: B 294 CYS cc_start: 0.8496 (m) cc_final: 0.8254 (t) REVERT: G 18 GLN cc_start: 0.8780 (tp40) cc_final: 0.8175 (tp40) REVERT: N 25 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8346 (p) REVERT: N 34 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.9043 (mmm) outliers start: 56 outliers final: 29 residues processed: 310 average time/residue: 0.7635 time to fit residues: 248.7321 Evaluate side-chains 312 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 273 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 404 ARG Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 79 optimal weight: 0.0970 chunk 82 optimal weight: 0.0030 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 358 ASN A 357 HIS B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.087499 restraints weight = 17934.547| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.68 r_work: 0.3154 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9396 Z= 0.120 Angle : 0.599 8.993 12720 Z= 0.312 Chirality : 0.042 0.202 1405 Planarity : 0.004 0.051 1617 Dihedral : 4.460 46.267 1260 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.36 % Allowed : 21.07 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.26), residues: 1123 helix: 2.11 (0.26), residues: 444 sheet: 0.31 (0.34), residues: 240 loop : -0.57 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 51 TYR 0.024 0.001 TYR R 191 PHE 0.013 0.001 PHE R 314 TRP 0.023 0.001 TRP R 164 HIS 0.002 0.000 HIS R 114 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9389) covalent geometry : angle 0.59862 (12708) SS BOND : bond 0.00216 ( 6) SS BOND : angle 1.12919 ( 12) hydrogen bonds : bond 0.04318 ( 464) hydrogen bonds : angle 4.17271 ( 1344) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 282 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8415 (tp30) cc_final: 0.7843 (tp30) REVERT: R 37 GLN cc_start: 0.8783 (tp40) cc_final: 0.8411 (tp-100) REVERT: R 39 PHE cc_start: 0.8954 (t80) cc_final: 0.8667 (t80) REVERT: R 40 LEU cc_start: 0.9342 (mm) cc_final: 0.9073 (tp) REVERT: R 135 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8464 (pp) REVERT: R 137 ASP cc_start: 0.7771 (m-30) cc_final: 0.7489 (m-30) REVERT: R 156 LEU cc_start: 0.7394 (mt) cc_final: 0.6660 (tt) REVERT: R 182 GLU cc_start: 0.7511 (tp30) cc_final: 0.7077 (tp30) REVERT: R 207 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8342 (mm) REVERT: R 407 LEU cc_start: 0.8341 (tp) cc_final: 0.8100 (tt) REVERT: R 425 MET cc_start: 0.8748 (ptm) cc_final: 0.8408 (ptm) REVERT: R 469 GLU cc_start: 0.8136 (tp30) cc_final: 0.7565 (tp30) REVERT: P 21 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8307 (ttm-80) REVERT: A 27 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: A 29 GLN cc_start: 0.8434 (tp-100) cc_final: 0.7919 (tm-30) REVERT: A 38 ARG cc_start: 0.8371 (mtm110) cc_final: 0.8122 (mtm110) REVERT: A 46 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8071 (tt) REVERT: A 53 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8236 (ttmm) REVERT: A 215 ASP cc_start: 0.7496 (m-30) cc_final: 0.7227 (t70) REVERT: A 271 LYS cc_start: 0.8416 (mmtp) cc_final: 0.8155 (mttp) REVERT: A 347 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8057 (ttm-80) REVERT: A 381 ASP cc_start: 0.8533 (t0) cc_final: 0.8274 (t0) REVERT: B 12 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7840 (pp20) REVERT: B 13 GLN cc_start: 0.8829 (mm110) cc_final: 0.8515 (mm-40) REVERT: B 19 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8359 (ttp80) REVERT: B 22 ARG cc_start: 0.8405 (mtt180) cc_final: 0.7917 (mtm180) REVERT: B 25 CYS cc_start: 0.8504 (m) cc_final: 0.8067 (p) REVERT: B 59 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: B 75 GLN cc_start: 0.8556 (mt0) cc_final: 0.8205 (mt0) REVERT: B 89 LYS cc_start: 0.8787 (mttp) cc_final: 0.8461 (mttp) REVERT: B 214 ARG cc_start: 0.8040 (ptp90) cc_final: 0.7570 (ptp90) REVERT: B 217 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7773 (tmm) REVERT: B 234 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8172 (m-80) REVERT: B 246 ASP cc_start: 0.8033 (m-30) cc_final: 0.7626 (m-30) REVERT: B 258 ASP cc_start: 0.8163 (t0) cc_final: 0.7301 (t0) REVERT: B 259 GLN cc_start: 0.8289 (mt0) cc_final: 0.7189 (mt0) REVERT: B 294 CYS cc_start: 0.8455 (m) cc_final: 0.8205 (t) REVERT: B 325 MET cc_start: 0.8718 (mmt) cc_final: 0.8491 (mmm) REVERT: G 18 GLN cc_start: 0.8728 (tp40) cc_final: 0.8128 (tp40) REVERT: G 54 VAL cc_start: 0.8997 (t) cc_final: 0.8781 (p) REVERT: N 13 GLN cc_start: 0.8331 (pp30) cc_final: 0.8072 (mm-40) REVERT: N 35 ASN cc_start: 0.8955 (m-40) cc_final: 0.8700 (m-40) outliers start: 43 outliers final: 20 residues processed: 299 average time/residue: 0.8086 time to fit residues: 253.2907 Evaluate side-chains 297 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 404 ARG Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS A 236 GLN A 357 HIS N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.101315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085481 restraints weight = 18112.851| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.67 r_work: 0.3118 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9396 Z= 0.180 Angle : 0.632 9.519 12720 Z= 0.328 Chirality : 0.044 0.224 1405 Planarity : 0.004 0.061 1617 Dihedral : 4.606 48.382 1260 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.27 % Allowed : 21.58 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1123 helix: 2.06 (0.25), residues: 450 sheet: 0.28 (0.33), residues: 240 loop : -0.64 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.023 0.001 TYR R 191 PHE 0.014 0.001 PHE B 151 TRP 0.025 0.002 TRP R 164 HIS 0.003 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9389) covalent geometry : angle 0.63150 (12708) SS BOND : bond 0.00235 ( 6) SS BOND : angle 1.16190 ( 12) hydrogen bonds : bond 0.04843 ( 464) hydrogen bonds : angle 4.23601 ( 1344) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 281 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8418 (tp30) cc_final: 0.7899 (tp30) REVERT: R 37 GLN cc_start: 0.8838 (tp40) cc_final: 0.8459 (tp-100) REVERT: R 39 PHE cc_start: 0.8992 (t80) cc_final: 0.8720 (t80) REVERT: R 40 LEU cc_start: 0.9343 (mm) cc_final: 0.9106 (tp) REVERT: R 135 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8484 (pp) REVERT: R 137 ASP cc_start: 0.7837 (m-30) cc_final: 0.7519 (m-30) REVERT: R 154 TRP cc_start: 0.6982 (m100) cc_final: 0.6755 (m100) REVERT: R 156 LEU cc_start: 0.7399 (mt) cc_final: 0.6724 (tt) REVERT: R 182 GLU cc_start: 0.7599 (tp30) cc_final: 0.7118 (tp30) REVERT: R 207 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8375 (mm) REVERT: R 213 ARG cc_start: 0.7901 (tpt-90) cc_final: 0.7675 (tpt-90) REVERT: R 407 LEU cc_start: 0.8378 (tp) cc_final: 0.8131 (tt) REVERT: R 425 MET cc_start: 0.8787 (ptm) cc_final: 0.8437 (ptm) REVERT: P 21 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8256 (ttm-80) REVERT: A 27 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: A 29 GLN cc_start: 0.8478 (tp-100) cc_final: 0.7946 (tm-30) REVERT: A 38 ARG cc_start: 0.8367 (mtm110) cc_final: 0.8134 (mtm110) REVERT: A 46 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8191 (tt) REVERT: A 53 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8238 (ttmm) REVERT: A 54 SER cc_start: 0.9296 (OUTLIER) cc_final: 0.8824 (p) REVERT: A 215 ASP cc_start: 0.7526 (m-30) cc_final: 0.7271 (t70) REVERT: A 347 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8210 (ttm-80) REVERT: B 22 ARG cc_start: 0.8475 (mtt180) cc_final: 0.7913 (mtm180) REVERT: B 25 CYS cc_start: 0.8440 (m) cc_final: 0.8051 (p) REVERT: B 59 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: B 75 GLN cc_start: 0.8496 (mt0) cc_final: 0.8168 (mt0) REVERT: B 89 LYS cc_start: 0.8789 (mttp) cc_final: 0.8474 (mttp) REVERT: B 172 GLU cc_start: 0.8407 (tp30) cc_final: 0.8019 (tp30) REVERT: B 197 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7903 (tpp80) REVERT: B 217 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7658 (tmm) REVERT: B 219 ARG cc_start: 0.8352 (tpp80) cc_final: 0.7970 (mmt90) REVERT: B 234 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: B 246 ASP cc_start: 0.8061 (m-30) cc_final: 0.7778 (m-30) REVERT: B 258 ASP cc_start: 0.8253 (t0) cc_final: 0.7284 (t0) REVERT: B 259 GLN cc_start: 0.8404 (mt0) cc_final: 0.7263 (mt0) REVERT: B 294 CYS cc_start: 0.8535 (m) cc_final: 0.8262 (t) REVERT: B 325 MET cc_start: 0.8775 (mmt) cc_final: 0.8573 (mmm) REVERT: G 18 GLN cc_start: 0.8740 (tp40) cc_final: 0.8000 (tp40) REVERT: G 42 GLU cc_start: 0.8441 (tt0) cc_final: 0.8232 (tt0) REVERT: N 115 TYR cc_start: 0.9035 (t80) cc_final: 0.8694 (t80) outliers start: 52 outliers final: 25 residues processed: 303 average time/residue: 0.7290 time to fit residues: 231.9154 Evaluate side-chains 308 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 404 ARG Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS A 278 ASN A 357 HIS N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083996 restraints weight = 18431.999| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.70 r_work: 0.3093 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9396 Z= 0.224 Angle : 0.672 9.725 12720 Z= 0.350 Chirality : 0.045 0.236 1405 Planarity : 0.004 0.058 1617 Dihedral : 4.757 49.278 1260 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.57 % Allowed : 22.70 % Favored : 71.73 % 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: 0.86 (0.26), residues: 1123 helix: 1.95 (0.25), residues: 450 sheet: 0.11 (0.32), residues: 256 loop : -0.60 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 96 TYR 0.023 0.002 TYR N 60 PHE 0.016 0.002 PHE B 151 TRP 0.027 0.002 TRP R 164 HIS 0.003 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 9389) covalent geometry : angle 0.67175 (12708) SS BOND : bond 0.00257 ( 6) SS BOND : angle 1.19158 ( 12) hydrogen bonds : bond 0.05214 ( 464) hydrogen bonds : angle 4.35814 ( 1344) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 279 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8506 (tp30) cc_final: 0.7946 (tp30) REVERT: R 37 GLN cc_start: 0.8957 (tp40) cc_final: 0.8539 (tp-100) REVERT: R 39 PHE cc_start: 0.9013 (t80) cc_final: 0.8713 (t80) REVERT: R 40 LEU cc_start: 0.9372 (mm) cc_final: 0.9115 (tp) REVERT: R 135 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8549 (pp) REVERT: R 137 ASP cc_start: 0.7840 (m-30) cc_final: 0.7489 (m-30) REVERT: R 182 GLU cc_start: 0.7691 (tp30) cc_final: 0.7210 (tp30) REVERT: R 207 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8400 (mm) REVERT: R 213 ARG cc_start: 0.7976 (tpt-90) cc_final: 0.7733 (tpt-90) REVERT: R 407 LEU cc_start: 0.8404 (tp) cc_final: 0.8159 (tt) REVERT: R 425 MET cc_start: 0.8837 (ptm) cc_final: 0.8521 (ptm) REVERT: P 21 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8265 (ttm-80) REVERT: A 27 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 29 GLN cc_start: 0.8518 (tp-100) cc_final: 0.7980 (tm-30) REVERT: A 38 ARG cc_start: 0.8383 (mtm110) cc_final: 0.8158 (mtm110) REVERT: A 46 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8234 (tt) REVERT: A 53 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8245 (ttmm) REVERT: A 54 SER cc_start: 0.9316 (OUTLIER) cc_final: 0.8858 (p) REVERT: A 215 ASP cc_start: 0.7613 (m-30) cc_final: 0.7342 (t70) REVERT: A 347 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8240 (ttm-80) REVERT: A 381 ASP cc_start: 0.8600 (t0) cc_final: 0.8310 (t0) REVERT: B 12 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7795 (pp20) REVERT: B 22 ARG cc_start: 0.8571 (mtt180) cc_final: 0.8052 (mtm180) REVERT: B 25 CYS cc_start: 0.8471 (m) cc_final: 0.8076 (p) REVERT: B 89 LYS cc_start: 0.8816 (mttp) cc_final: 0.8527 (mttp) REVERT: B 172 GLU cc_start: 0.8445 (tp30) cc_final: 0.8057 (tp30) REVERT: B 197 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7910 (tpp80) REVERT: B 215 GLU cc_start: 0.8307 (mp0) cc_final: 0.7741 (mp0) REVERT: B 217 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7728 (tmm) REVERT: B 219 ARG cc_start: 0.8380 (tpp80) cc_final: 0.8065 (mmt90) REVERT: B 234 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: B 246 ASP cc_start: 0.8145 (m-30) cc_final: 0.7887 (m-30) REVERT: B 258 ASP cc_start: 0.8301 (t0) cc_final: 0.7417 (t0) REVERT: B 259 GLN cc_start: 0.8418 (mt0) cc_final: 0.7306 (mt0) REVERT: B 294 CYS cc_start: 0.8604 (m) cc_final: 0.8266 (t) REVERT: G 42 GLU cc_start: 0.8465 (tt0) cc_final: 0.8259 (tt0) REVERT: N 13 GLN cc_start: 0.8334 (pp30) cc_final: 0.8046 (mm-40) outliers start: 55 outliers final: 33 residues processed: 301 average time/residue: 0.7273 time to fit residues: 230.0158 Evaluate side-chains 320 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 404 ARG Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 47 GLN R 114 HIS R 358 ASN A 278 ASN A 357 HIS B 75 GLN G 18 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.099216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.083496 restraints weight = 18213.190| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.70 r_work: 0.3083 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9396 Z= 0.243 Angle : 0.702 10.838 12720 Z= 0.364 Chirality : 0.046 0.254 1405 Planarity : 0.005 0.056 1617 Dihedral : 4.834 48.189 1260 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.86 % Allowed : 24.32 % Favored : 70.82 % 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: 0.69 (0.26), residues: 1123 helix: 1.78 (0.25), residues: 455 sheet: 0.01 (0.32), residues: 259 loop : -0.70 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 43 TYR 0.024 0.002 TYR N 60 PHE 0.017 0.002 PHE B 151 TRP 0.029 0.002 TRP R 164 HIS 0.004 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 9389) covalent geometry : angle 0.70168 (12708) SS BOND : bond 0.00317 ( 6) SS BOND : angle 1.27153 ( 12) hydrogen bonds : bond 0.05320 ( 464) hydrogen bonds : angle 4.43278 ( 1344) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8542 (tp30) cc_final: 0.7961 (tp30) REVERT: R 37 GLN cc_start: 0.9000 (tp40) cc_final: 0.8570 (tp-100) REVERT: R 39 PHE cc_start: 0.9043 (t80) cc_final: 0.8474 (t80) REVERT: R 40 LEU cc_start: 0.9376 (mm) cc_final: 0.9137 (tp) REVERT: R 137 ASP cc_start: 0.7854 (m-30) cc_final: 0.7509 (m-30) REVERT: R 156 LEU cc_start: 0.7057 (mt) cc_final: 0.6324 (tt) REVERT: R 182 GLU cc_start: 0.7698 (tp30) cc_final: 0.7250 (tp30) REVERT: R 207 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8397 (mm) REVERT: R 213 ARG cc_start: 0.7999 (tpt-90) cc_final: 0.7735 (tpt-90) REVERT: R 407 LEU cc_start: 0.8353 (tp) cc_final: 0.8103 (tt) REVERT: R 425 MET cc_start: 0.8846 (ptm) cc_final: 0.8518 (ptm) REVERT: R 463 ASN cc_start: 0.8083 (t0) cc_final: 0.7744 (t0) REVERT: P 21 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8268 (ttm-80) REVERT: A 27 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: A 29 GLN cc_start: 0.8531 (tp-100) cc_final: 0.8040 (tm-30) REVERT: A 38 ARG cc_start: 0.8405 (mtm110) cc_final: 0.8175 (mtm110) REVERT: A 46 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8223 (tt) REVERT: A 53 LYS cc_start: 0.8452 (ttpp) cc_final: 0.8243 (ttmm) REVERT: A 54 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.8940 (t) REVERT: A 271 LYS cc_start: 0.8524 (mmtp) cc_final: 0.8262 (mttp) REVERT: A 347 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.8263 (ttm-80) REVERT: A 381 ASP cc_start: 0.8604 (t0) cc_final: 0.8325 (t0) REVERT: B 12 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7878 (pp20) REVERT: B 22 ARG cc_start: 0.8591 (mtt180) cc_final: 0.8040 (mtm180) REVERT: B 25 CYS cc_start: 0.8462 (m) cc_final: 0.8041 (p) REVERT: B 75 GLN cc_start: 0.8512 (mt0) cc_final: 0.8234 (mt0) REVERT: B 89 LYS cc_start: 0.8834 (mttp) cc_final: 0.8545 (mttp) REVERT: B 172 GLU cc_start: 0.8481 (tp30) cc_final: 0.8066 (tp30) REVERT: B 215 GLU cc_start: 0.8365 (mp0) cc_final: 0.7816 (mp0) REVERT: B 217 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7776 (tmm) REVERT: B 219 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8080 (mmt90) REVERT: B 234 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: B 246 ASP cc_start: 0.8165 (m-30) cc_final: 0.7909 (m-30) REVERT: B 258 ASP cc_start: 0.8216 (t0) cc_final: 0.7371 (t0) REVERT: B 259 GLN cc_start: 0.8458 (mt0) cc_final: 0.7303 (mt0) REVERT: B 294 CYS cc_start: 0.8633 (m) cc_final: 0.8248 (t) REVERT: N 115 TYR cc_start: 0.9064 (t80) cc_final: 0.8712 (t80) outliers start: 48 outliers final: 31 residues processed: 302 average time/residue: 0.7381 time to fit residues: 233.9457 Evaluate side-chains 314 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 404 ARG Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS A 278 ASN A 357 HIS A 384 GLN G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.100627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.084968 restraints weight = 17977.182| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.66 r_work: 0.3112 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9396 Z= 0.172 Angle : 0.694 10.006 12720 Z= 0.357 Chirality : 0.045 0.256 1405 Planarity : 0.004 0.051 1617 Dihedral : 4.704 46.079 1260 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.44 % Allowed : 26.55 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1123 helix: 1.95 (0.25), residues: 448 sheet: 0.24 (0.32), residues: 251 loop : -0.62 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 51 TYR 0.023 0.001 TYR N 60 PHE 0.014 0.001 PHE A 212 TRP 0.037 0.002 TRP R 164 HIS 0.008 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9389) covalent geometry : angle 0.69350 (12708) SS BOND : bond 0.00297 ( 6) SS BOND : angle 1.21812 ( 12) hydrogen bonds : bond 0.04840 ( 464) hydrogen bonds : angle 4.32859 ( 1344) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8466 (tp30) cc_final: 0.7887 (tp30) REVERT: R 37 GLN cc_start: 0.8962 (tp40) cc_final: 0.8535 (tp-100) REVERT: R 39 PHE cc_start: 0.8900 (t80) cc_final: 0.8685 (t80) REVERT: R 40 LEU cc_start: 0.9335 (mm) cc_final: 0.9117 (tp) REVERT: R 137 ASP cc_start: 0.7835 (m-30) cc_final: 0.7542 (m-30) REVERT: R 156 LEU cc_start: 0.7087 (mt) cc_final: 0.6372 (tt) REVERT: R 182 GLU cc_start: 0.7637 (tp30) cc_final: 0.7151 (tp30) REVERT: R 207 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8391 (mm) REVERT: R 407 LEU cc_start: 0.8385 (tp) cc_final: 0.8154 (tt) REVERT: R 425 MET cc_start: 0.8825 (ptm) cc_final: 0.8510 (ptm) REVERT: R 463 ASN cc_start: 0.8055 (t0) cc_final: 0.7697 (t0) REVERT: P 21 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8252 (ttm-80) REVERT: A 27 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: A 29 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8023 (tm-30) REVERT: A 38 ARG cc_start: 0.8374 (mtm110) cc_final: 0.8150 (mtm110) REVERT: A 46 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8175 (tt) REVERT: A 53 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8248 (ttmm) REVERT: A 54 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.8880 (p) REVERT: A 215 ASP cc_start: 0.7635 (m-30) cc_final: 0.7374 (t70) REVERT: A 271 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8275 (mttp) REVERT: A 347 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8255 (ttm-80) REVERT: A 381 ASP cc_start: 0.8605 (t0) cc_final: 0.8324 (t0) REVERT: B 12 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7952 (pp20) REVERT: B 13 GLN cc_start: 0.8840 (mm110) cc_final: 0.8481 (mm-40) REVERT: B 22 ARG cc_start: 0.8589 (mtt180) cc_final: 0.8048 (mtm180) REVERT: B 25 CYS cc_start: 0.8431 (m) cc_final: 0.8075 (p) REVERT: B 75 GLN cc_start: 0.8501 (mt0) cc_final: 0.8228 (mt0) REVERT: B 89 LYS cc_start: 0.8862 (mttp) cc_final: 0.8609 (mttp) REVERT: B 172 GLU cc_start: 0.8476 (tp30) cc_final: 0.8068 (tp30) REVERT: B 215 GLU cc_start: 0.8354 (mp0) cc_final: 0.7826 (mp0) REVERT: B 217 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7777 (tmm) REVERT: B 219 ARG cc_start: 0.8383 (tpp80) cc_final: 0.8069 (mmt90) REVERT: B 234 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: B 246 ASP cc_start: 0.8134 (m-30) cc_final: 0.7877 (m-30) REVERT: B 258 ASP cc_start: 0.8218 (t0) cc_final: 0.7369 (t0) REVERT: B 259 GLN cc_start: 0.8412 (mt0) cc_final: 0.7280 (mt0) REVERT: B 275 SER cc_start: 0.9022 (p) cc_final: 0.8796 (p) REVERT: B 294 CYS cc_start: 0.8563 (m) cc_final: 0.8199 (t) REVERT: N 13 GLN cc_start: 0.8385 (pp30) cc_final: 0.8007 (mm-40) REVERT: N 35 ASN cc_start: 0.9111 (m-40) cc_final: 0.8814 (m110) outliers start: 34 outliers final: 26 residues processed: 298 average time/residue: 0.7366 time to fit residues: 230.5313 Evaluate side-chains 312 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS R 358 ASN A 357 HIS A 384 GLN B 17 GLN B 32 GLN G 18 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.101141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085532 restraints weight = 18193.442| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.68 r_work: 0.3126 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9396 Z= 0.152 Angle : 0.691 10.049 12720 Z= 0.356 Chirality : 0.044 0.252 1405 Planarity : 0.005 0.052 1617 Dihedral : 4.631 45.353 1260 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.34 % Allowed : 26.24 % Favored : 70.42 % 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: 0.94 (0.26), residues: 1123 helix: 2.00 (0.25), residues: 443 sheet: 0.34 (0.33), residues: 245 loop : -0.63 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 51 TYR 0.023 0.001 TYR R 191 PHE 0.014 0.001 PHE A 212 TRP 0.043 0.002 TRP R 164 HIS 0.003 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9389) covalent geometry : angle 0.69087 (12708) SS BOND : bond 0.00213 ( 6) SS BOND : angle 1.10471 ( 12) hydrogen bonds : bond 0.04584 ( 464) hydrogen bonds : angle 4.29877 ( 1344) Misc. bond : bond 0.00004 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8452 (tp30) cc_final: 0.7877 (tp30) REVERT: R 37 GLN cc_start: 0.8958 (tp40) cc_final: 0.8532 (tp-100) REVERT: R 39 PHE cc_start: 0.8887 (t80) cc_final: 0.8605 (t80) REVERT: R 137 ASP cc_start: 0.7848 (m-30) cc_final: 0.7566 (m-30) REVERT: R 156 LEU cc_start: 0.7015 (mt) cc_final: 0.6343 (tt) REVERT: R 182 GLU cc_start: 0.7612 (tp30) cc_final: 0.7123 (tp30) REVERT: R 207 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8372 (mm) REVERT: R 407 LEU cc_start: 0.8375 (tp) cc_final: 0.8140 (tt) REVERT: R 425 MET cc_start: 0.8799 (ptm) cc_final: 0.8505 (ptm) REVERT: R 463 ASN cc_start: 0.7951 (t0) cc_final: 0.7670 (t0) REVERT: P 21 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8263 (ttm-80) REVERT: A 27 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: A 29 GLN cc_start: 0.8525 (tp-100) cc_final: 0.8049 (tm-30) REVERT: A 38 ARG cc_start: 0.8356 (mtm110) cc_final: 0.8148 (mtm110) REVERT: A 46 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8112 (tt) REVERT: A 54 SER cc_start: 0.9405 (OUTLIER) cc_final: 0.8961 (p) REVERT: A 271 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8276 (mttp) REVERT: A 333 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7760 (mtm-85) REVERT: A 381 ASP cc_start: 0.8611 (t0) cc_final: 0.8304 (t0) REVERT: B 22 ARG cc_start: 0.8605 (mtt180) cc_final: 0.7771 (mtt180) REVERT: B 25 CYS cc_start: 0.8432 (m) cc_final: 0.8082 (p) REVERT: B 89 LYS cc_start: 0.8853 (mttp) cc_final: 0.8580 (mttp) REVERT: B 172 GLU cc_start: 0.8478 (tp30) cc_final: 0.8078 (tp30) REVERT: B 215 GLU cc_start: 0.8352 (mp0) cc_final: 0.7830 (mp0) REVERT: B 217 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7806 (tmm) REVERT: B 219 ARG cc_start: 0.8384 (tpp80) cc_final: 0.8088 (mmt90) REVERT: B 234 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: B 246 ASP cc_start: 0.8136 (m-30) cc_final: 0.7881 (m-30) REVERT: B 258 ASP cc_start: 0.8208 (t0) cc_final: 0.7166 (t0) REVERT: B 259 GLN cc_start: 0.8419 (mt0) cc_final: 0.7284 (mt0) REVERT: B 275 SER cc_start: 0.9021 (p) cc_final: 0.8796 (p) REVERT: B 294 CYS cc_start: 0.8555 (m) cc_final: 0.8186 (t) REVERT: N 13 GLN cc_start: 0.8381 (pp30) cc_final: 0.8021 (mm-40) outliers start: 33 outliers final: 26 residues processed: 300 average time/residue: 0.7265 time to fit residues: 229.2012 Evaluate side-chains 312 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS A 357 HIS A 384 GLN B 32 GLN G 18 GLN N 31 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085888 restraints weight = 17860.216| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.64 r_work: 0.3125 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9396 Z= 0.167 Angle : 0.704 9.572 12720 Z= 0.364 Chirality : 0.045 0.253 1405 Planarity : 0.004 0.054 1617 Dihedral : 4.631 45.541 1260 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.95 % Allowed : 26.14 % Favored : 69.91 % 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: 0.87 (0.26), residues: 1123 helix: 1.90 (0.25), residues: 443 sheet: 0.35 (0.33), residues: 245 loop : -0.65 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 51 TYR 0.023 0.001 TYR R 191 PHE 0.014 0.001 PHE A 212 TRP 0.042 0.002 TRP R 164 HIS 0.004 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9389) covalent geometry : angle 0.70357 (12708) SS BOND : bond 0.00208 ( 6) SS BOND : angle 1.07493 ( 12) hydrogen bonds : bond 0.04658 ( 464) hydrogen bonds : angle 4.34594 ( 1344) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4404.18 seconds wall clock time: 75 minutes 26.55 seconds (4526.55 seconds total)