Starting phenix.real_space_refine on Thu Mar 13 20:15:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y35_33588/03_2025/7y35_33588.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y35_33588/03_2025/7y35_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_2025/7y35_33588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y35_33588/03_2025/7y35_33588.map" model { file = "/net/cci-nas-00/data/ceres_data/7y35_33588/03_2025/7y35_33588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y35_33588/03_2025/7y35_33588.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.37, per 1000 atoms: 0.58 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: 2.25 Conformation dependent library (CDL) restraints added in 995.6 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: 0.97 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: 2.49 Time building geometry restraints manager: 2.66 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.950 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.860 ------------------------------------------------------------------------------- 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 0.071 9389 Z= 0.586 Angle : 0.795 17.243 12708 Z= 0.477 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 : 5.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.003 TRP B 99 HIS 0.016 0.002 HIS A 357 PHE 0.022 0.002 PHE R 335 TYR 0.042 0.002 TYR B 59 ARG 0.005 0.001 ARG R 400 *********************** 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 : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8776 (mp0) cc_final: 0.8368 (mp0) REVERT: R 36 GLU cc_start: 0.8431 (tp30) cc_final: 0.7972 (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: 0.7222 (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: 0.8138 (mmtm) cc_final: 0.7857 (mmtm) REVERT: A 27 GLU cc_start: 0.7022 (mp0) cc_final: 0.6815 (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: 0.8293 (mtt-85) REVERT: B 215 GLU cc_start: 0.7835 (mp0) cc_final: 0.7546 (mp0) REVERT: B 254 ASP cc_start: 0.7917 (m-30) cc_final: 0.7693 (m-30) REVERT: B 258 ASP cc_start: 0.7908 (t0) cc_final: 0.6962 (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: 0.8084 (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: 0.8384 (tm-30) REVERT: N 125 THR cc_start: 0.8250 (p) cc_final: 0.7520 (p) outliers start: 1 outliers final: 0 residues processed: 345 average time/residue: 1.5158 time to fit residues: 550.4252 Evaluate side-chains 286 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 155 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.106380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.090246 restraints weight = 17854.134| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.70 r_work: 0.3215 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9389 Z= 0.201 Angle : 0.608 7.618 12708 Z= 0.323 Chirality : 0.043 0.236 1405 Planarity : 0.005 0.059 1617 Dihedral : 4.940 52.044 1260 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.44 % Allowed : 16.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1123 helix: 1.07 (0.25), residues: 456 sheet: -0.17 (0.33), residues: 229 loop : -1.36 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 352 HIS 0.004 0.001 HIS R 114 PHE 0.020 0.001 PHE R 314 TYR 0.026 0.001 TYR R 191 ARG 0.008 0.001 ARG A 342 *********************** 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 334 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 GLN cc_start: 0.8764 (tp40) cc_final: 0.8444 (tp40) REVERT: R 39 PHE cc_start: 0.9016 (t80) cc_final: 0.8657 (t80) REVERT: R 43 ARG cc_start: 0.8540 (mmm160) cc_final: 0.8253 (mmm160) REVERT: R 156 LEU cc_start: 0.7271 (mt) cc_final: 0.6834 (tt) REVERT: R 160 HIS cc_start: 0.7400 (m90) cc_final: 0.6991 (m90) REVERT: R 182 GLU cc_start: 0.7398 (tp30) cc_final: 0.7042 (tp30) REVERT: R 207 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8369 (mm) REVERT: R 346 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8600 (mt) REVERT: R 407 LEU cc_start: 0.8288 (tp) cc_final: 0.7977 (tt) REVERT: R 425 MET cc_start: 0.8732 (ptm) cc_final: 0.8532 (ptm) REVERT: P 27 LEU cc_start: 0.8831 (mm) cc_final: 0.8590 (mm) REVERT: A 17 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7960 (mmtm) REVERT: A 27 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: A 34 LYS cc_start: 0.8989 (tttt) cc_final: 0.8662 (ttmm) REVERT: A 38 ARG cc_start: 0.8327 (mtm110) cc_final: 0.8045 (mtm110) REVERT: A 46 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8091 (tt) REVERT: A 53 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8141 (ttpp) REVERT: A 54 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8818 (t) REVERT: A 240 ASP cc_start: 0.7620 (m-30) cc_final: 0.7384 (m-30) REVERT: A 280 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8630 (ttpp) REVERT: A 311 TYR cc_start: 0.8419 (m-80) cc_final: 0.8119 (m-80) REVERT: A 343 ASP cc_start: 0.8665 (m-30) cc_final: 0.8369 (m-30) REVERT: B 12 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7872 (pp20) REVERT: B 22 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7516 (mtm-85) REVERT: B 25 CYS cc_start: 0.8440 (m) cc_final: 0.7936 (p) REVERT: B 32 GLN cc_start: 0.8402 (mt0) cc_final: 0.8086 (mt0) REVERT: B 46 ARG cc_start: 0.8494 (mtp180) cc_final: 0.7980 (ttm110) REVERT: B 75 GLN cc_start: 0.8697 (mt0) cc_final: 0.8408 (mt0) REVERT: B 89 LYS cc_start: 0.8803 (mttp) cc_final: 0.8388 (mttp) REVERT: B 134 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7592 (mtm-85) REVERT: B 214 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7679 (ptp90) REVERT: B 215 GLU cc_start: 0.8229 (mp0) cc_final: 0.7929 (mp0) REVERT: B 258 ASP cc_start: 0.8266 (t0) cc_final: 0.6895 (t0) REVERT: B 294 CYS cc_start: 0.8527 (m) cc_final: 0.8268 (t) REVERT: G 42 GLU cc_start: 0.8493 (tt0) cc_final: 0.8271 (tt0) REVERT: N 69 THR cc_start: 0.8820 (m) cc_final: 0.8435 (p) REVERT: N 78 THR cc_start: 0.9034 (t) cc_final: 0.8753 (p) outliers start: 34 outliers final: 17 residues processed: 311 average time/residue: 1.4682 time to fit residues: 481.8137 Evaluate side-chains 306 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 284 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 244 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 A residue 327 GLU Chi-restraints excluded: chain B residue 18 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 0.0770 chunk 41 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.106632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090450 restraints weight = 18249.484| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.73 r_work: 0.3213 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9389 Z= 0.166 Angle : 0.581 8.838 12708 Z= 0.303 Chirality : 0.042 0.237 1405 Planarity : 0.004 0.054 1617 Dihedral : 4.528 45.206 1260 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.75 % Allowed : 19.15 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1123 helix: 1.64 (0.25), residues: 455 sheet: 0.05 (0.34), residues: 240 loop : -0.99 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 164 HIS 0.003 0.001 HIS A 357 PHE 0.019 0.001 PHE R 314 TYR 0.025 0.001 TYR R 191 ARG 0.009 0.001 ARG R 150 *********************** 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 325 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8457 (tp30) cc_final: 0.7818 (tp30) REVERT: R 37 GLN cc_start: 0.8783 (tp40) cc_final: 0.8433 (tp40) REVERT: R 39 PHE cc_start: 0.9012 (t80) cc_final: 0.8666 (t80) REVERT: R 40 LEU cc_start: 0.9360 (mm) cc_final: 0.8891 (mm) REVERT: R 156 LEU cc_start: 0.7282 (mt) cc_final: 0.6728 (tt) REVERT: R 160 HIS cc_start: 0.7527 (m90) cc_final: 0.7185 (m90) REVERT: R 182 GLU cc_start: 0.7356 (tp30) cc_final: 0.6949 (tp30) REVERT: R 207 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8357 (mm) REVERT: R 346 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8639 (mt) REVERT: R 407 LEU cc_start: 0.8277 (tp) cc_final: 0.7986 (tt) REVERT: R 425 MET cc_start: 0.8717 (ptm) cc_final: 0.8311 (ptm) REVERT: A 17 LYS cc_start: 0.8325 (mmtm) cc_final: 0.8073 (mmtm) REVERT: A 27 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: A 34 LYS cc_start: 0.8958 (tttt) cc_final: 0.8677 (ttmm) REVERT: A 38 ARG cc_start: 0.8323 (mtm110) cc_final: 0.8064 (mtm110) REVERT: A 46 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8072 (tt) REVERT: A 311 TYR cc_start: 0.8452 (m-80) cc_final: 0.8142 (m-80) REVERT: A 333 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7642 (mtm-85) REVERT: A 343 ASP cc_start: 0.8640 (m-30) cc_final: 0.8260 (m-30) REVERT: B 12 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7970 (pp20) REVERT: B 13 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8377 (mm110) REVERT: B 25 CYS cc_start: 0.8431 (m) cc_final: 0.8021 (p) REVERT: B 32 GLN cc_start: 0.8344 (mt0) cc_final: 0.7980 (mt0) REVERT: B 57 LYS cc_start: 0.9102 (mtmm) cc_final: 0.8631 (pttp) REVERT: B 75 GLN cc_start: 0.8612 (mt0) cc_final: 0.8162 (mt0) REVERT: B 89 LYS cc_start: 0.8793 (mttp) cc_final: 0.8495 (mttp) REVERT: B 134 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7633 (mtm-85) REVERT: B 214 ARG cc_start: 0.8093 (ptp90) cc_final: 0.7640 (ptp90) REVERT: B 215 GLU cc_start: 0.8234 (mp0) cc_final: 0.7993 (mp0) REVERT: B 234 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: B 258 ASP cc_start: 0.8203 (t0) cc_final: 0.7828 (t0) REVERT: B 275 SER cc_start: 0.8910 (m) cc_final: 0.8707 (p) REVERT: B 294 CYS cc_start: 0.8555 (m) cc_final: 0.8316 (t) REVERT: G 42 GLU cc_start: 0.8529 (tt0) cc_final: 0.8305 (tt0) REVERT: N 35 ASN cc_start: 0.8938 (m-40) cc_final: 0.8682 (m-40) REVERT: N 69 THR cc_start: 0.8841 (m) cc_final: 0.8466 (p) REVERT: N 78 THR cc_start: 0.9130 (t) cc_final: 0.8828 (p) outliers start: 37 outliers final: 17 residues processed: 303 average time/residue: 1.4129 time to fit residues: 451.9108 Evaluate side-chains 301 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 279 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 163 THR 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 444 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 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 70 LEU 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 25 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 4.9990 chunk 69 optimal weight: 0.0270 chunk 23 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.105929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090074 restraints weight = 18078.848| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.69 r_work: 0.3203 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9389 Z= 0.177 Angle : 0.575 8.348 12708 Z= 0.299 Chirality : 0.042 0.190 1405 Planarity : 0.004 0.050 1617 Dihedral : 4.392 44.795 1260 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.95 % Allowed : 19.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1123 helix: 1.99 (0.26), residues: 450 sheet: 0.31 (0.34), residues: 239 loop : -0.77 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 164 HIS 0.002 0.001 HIS R 114 PHE 0.011 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.009 0.001 ARG P 21 *********************** 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 326 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 287 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8467 (tp30) cc_final: 0.7957 (tp30) REVERT: R 37 GLN cc_start: 0.8820 (tp40) cc_final: 0.8488 (tp40) REVERT: R 39 PHE cc_start: 0.8996 (t80) cc_final: 0.8654 (t80) REVERT: R 40 LEU cc_start: 0.9361 (mm) cc_final: 0.9087 (tp) REVERT: R 137 ASP cc_start: 0.7677 (m-30) cc_final: 0.7034 (m-30) REVERT: R 156 LEU cc_start: 0.7193 (mt) cc_final: 0.6636 (tt) REVERT: R 160 HIS cc_start: 0.7497 (m90) cc_final: 0.7182 (m90) REVERT: R 182 GLU cc_start: 0.7461 (tp30) cc_final: 0.7055 (tp30) REVERT: R 407 LEU cc_start: 0.8310 (tp) cc_final: 0.8059 (tt) REVERT: R 425 MET cc_start: 0.8744 (ptm) cc_final: 0.8354 (ptm) REVERT: P 21 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.8373 (tpp80) REVERT: P 26 LYS cc_start: 0.8771 (tmmt) cc_final: 0.8568 (tmmt) REVERT: A 17 LYS cc_start: 0.8372 (mmtm) cc_final: 0.8148 (mmtm) REVERT: A 27 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: A 38 ARG cc_start: 0.8343 (mtm110) cc_final: 0.8086 (mtm110) REVERT: A 46 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8007 (tt) REVERT: A 311 TYR cc_start: 0.8453 (m-80) cc_final: 0.8136 (m-80) REVERT: A 318 TYR cc_start: 0.8087 (t80) cc_final: 0.7840 (t80) REVERT: A 343 ASP cc_start: 0.8634 (m-30) cc_final: 0.8274 (m-30) REVERT: B 5 ASP cc_start: 0.8151 (p0) cc_final: 0.7739 (p0) REVERT: B 25 CYS cc_start: 0.8423 (m) cc_final: 0.8094 (p) REVERT: B 32 GLN cc_start: 0.8339 (mt0) cc_final: 0.7996 (mt0) REVERT: B 75 GLN cc_start: 0.8611 (mt0) cc_final: 0.8297 (mt0) REVERT: B 89 LYS cc_start: 0.8793 (mttp) cc_final: 0.8452 (mttp) REVERT: B 134 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: B 197 ARG cc_start: 0.8087 (mpt-90) cc_final: 0.7885 (tpp80) REVERT: B 215 GLU cc_start: 0.8257 (mp0) cc_final: 0.8021 (mp0) REVERT: B 219 ARG cc_start: 0.8479 (tpp80) cc_final: 0.8148 (mmt90) REVERT: B 234 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: B 254 ASP cc_start: 0.7751 (t0) cc_final: 0.7506 (t0) REVERT: B 258 ASP cc_start: 0.8297 (t0) cc_final: 0.7336 (t0) REVERT: B 294 CYS cc_start: 0.8527 (m) cc_final: 0.8295 (t) REVERT: G 18 GLN cc_start: 0.8695 (tp40) cc_final: 0.8035 (tp40) REVERT: G 21 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8170 (mtp) REVERT: G 42 GLU cc_start: 0.8532 (tt0) cc_final: 0.8305 (tt0) REVERT: N 35 ASN cc_start: 0.8956 (m-40) cc_final: 0.8710 (m-40) REVERT: N 69 THR cc_start: 0.8886 (m) cc_final: 0.8552 (p) REVERT: N 78 THR cc_start: 0.9163 (t) cc_final: 0.8828 (p) REVERT: N 95 TYR cc_start: 0.8972 (m-80) cc_final: 0.8376 (m-80) REVERT: N 114 THR cc_start: 0.8951 (t) cc_final: 0.8616 (p) outliers start: 39 outliers final: 17 residues processed: 302 average time/residue: 1.6172 time to fit residues: 515.3132 Evaluate side-chains 303 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 282 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 414 MET 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 57 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 349 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 0.0170 chunk 6 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS P 32 HIS A 236 GLN A 357 HIS B 220 GLN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.103882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087588 restraints weight = 18118.679| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.71 r_work: 0.3151 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9389 Z= 0.217 Angle : 0.586 8.620 12708 Z= 0.307 Chirality : 0.042 0.180 1405 Planarity : 0.004 0.050 1617 Dihedral : 4.372 44.964 1260 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.26 % Allowed : 21.38 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1123 helix: 2.09 (0.25), residues: 450 sheet: 0.45 (0.34), residues: 237 loop : -0.65 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 164 HIS 0.002 0.001 HIS B 91 PHE 0.021 0.001 PHE R 314 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.001 ARG B 96 *********************** 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 316 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8470 (tp30) cc_final: 0.7904 (tp30) REVERT: R 37 GLN cc_start: 0.8814 (tp40) cc_final: 0.8422 (tp-100) REVERT: R 39 PHE cc_start: 0.8990 (t80) cc_final: 0.8660 (t80) REVERT: R 40 LEU cc_start: 0.9347 (mm) cc_final: 0.9116 (tp) REVERT: R 137 ASP cc_start: 0.7885 (m-30) cc_final: 0.7001 (m-30) REVERT: R 156 LEU cc_start: 0.7298 (mt) cc_final: 0.6707 (tt) REVERT: R 160 HIS cc_start: 0.7529 (m90) cc_final: 0.7221 (m90) REVERT: R 182 GLU cc_start: 0.7586 (tp30) cc_final: 0.7152 (tp30) REVERT: R 405 LYS cc_start: 0.8386 (tppp) cc_final: 0.8077 (tppp) REVERT: R 407 LEU cc_start: 0.8301 (tp) cc_final: 0.8063 (tt) REVERT: R 414 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8487 (mmm) REVERT: R 425 MET cc_start: 0.8773 (ptm) cc_final: 0.8409 (ptm) REVERT: R 431 GLU cc_start: 0.7600 (tp30) cc_final: 0.7388 (tp30) REVERT: P 21 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8369 (tpp80) REVERT: A 17 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8197 (mmtm) REVERT: A 27 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: A 38 ARG cc_start: 0.8390 (mtm110) cc_final: 0.8136 (mtm110) REVERT: A 46 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7963 (tt) REVERT: A 271 LYS cc_start: 0.8492 (mmtm) cc_final: 0.8220 (mttp) REVERT: B 12 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7762 (pp20) REVERT: B 25 CYS cc_start: 0.8436 (m) cc_final: 0.8094 (p) REVERT: B 32 GLN cc_start: 0.8373 (mt0) cc_final: 0.8036 (mt0) REVERT: B 59 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8569 (m-80) REVERT: B 75 GLN cc_start: 0.8519 (mt0) cc_final: 0.8269 (mt0) REVERT: B 89 LYS cc_start: 0.8778 (mttp) cc_final: 0.8454 (mttp) REVERT: B 134 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7716 (mtm-85) REVERT: B 197 ARG cc_start: 0.8126 (mpt-90) cc_final: 0.7908 (tpp80) REVERT: B 215 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: B 234 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: B 254 ASP cc_start: 0.7857 (t0) cc_final: 0.7601 (OUTLIER) REVERT: B 258 ASP cc_start: 0.8275 (t0) cc_final: 0.7365 (t0) REVERT: B 294 CYS cc_start: 0.8473 (m) cc_final: 0.8245 (t) REVERT: G 42 GLU cc_start: 0.8504 (tt0) cc_final: 0.8293 (tt0) REVERT: N 35 ASN cc_start: 0.8975 (m-40) cc_final: 0.8709 (m-40) REVERT: N 90 ASP cc_start: 0.8827 (m-30) cc_final: 0.8613 (m-30) outliers start: 42 outliers final: 23 residues processed: 287 average time/residue: 1.7949 time to fit residues: 542.9588 Evaluate side-chains 300 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 414 MET 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 35 GLN Chi-restraints excluded: chain A residue 46 LEU 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 A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 215 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 31 optimal weight: 0.0030 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 N 31 ASN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088260 restraints weight = 18038.568| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.69 r_work: 0.3168 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9389 Z= 0.181 Angle : 0.585 8.782 12708 Z= 0.303 Chirality : 0.042 0.195 1405 Planarity : 0.004 0.049 1617 Dihedral : 4.261 43.333 1260 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.05 % Allowed : 22.70 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1123 helix: 2.30 (0.25), residues: 444 sheet: 0.51 (0.34), residues: 241 loop : -0.47 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 164 HIS 0.002 0.001 HIS R 42 PHE 0.018 0.001 PHE R 314 TYR 0.023 0.001 TYR R 191 ARG 0.011 0.001 ARG A 317 *********************** 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 328 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8409 (tp30) cc_final: 0.7897 (tp30) REVERT: R 37 GLN cc_start: 0.8791 (tp40) cc_final: 0.8424 (tp-100) REVERT: R 39 PHE cc_start: 0.8978 (t80) cc_final: 0.8692 (t80) REVERT: R 40 LEU cc_start: 0.9352 (mm) cc_final: 0.9103 (tp) REVERT: R 129 VAL cc_start: 0.8488 (t) cc_final: 0.8279 (p) REVERT: R 137 ASP cc_start: 0.7882 (m-30) cc_final: 0.7272 (m-30) REVERT: R 154 TRP cc_start: 0.6937 (m100) cc_final: 0.6729 (m100) REVERT: R 156 LEU cc_start: 0.7374 (mt) cc_final: 0.6701 (tt) REVERT: R 160 HIS cc_start: 0.7495 (m90) cc_final: 0.7183 (m90) REVERT: R 182 GLU cc_start: 0.7496 (tp30) cc_final: 0.7022 (tp30) REVERT: R 281 CYS cc_start: 0.5706 (OUTLIER) cc_final: 0.5485 (t) REVERT: R 407 LEU cc_start: 0.8300 (tp) cc_final: 0.8063 (tt) REVERT: R 425 MET cc_start: 0.8772 (ptm) cc_final: 0.8421 (ptm) REVERT: A 17 LYS cc_start: 0.8395 (mmtm) cc_final: 0.8187 (mmtm) REVERT: A 27 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: A 38 ARG cc_start: 0.8385 (mtm110) cc_final: 0.8149 (mtm110) REVERT: A 55 THR cc_start: 0.8788 (m) cc_final: 0.8543 (p) REVERT: A 223 ASP cc_start: 0.8159 (t0) cc_final: 0.7896 (t0) REVERT: A 271 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8187 (mttp) REVERT: A 381 ASP cc_start: 0.8535 (t0) cc_final: 0.8275 (t0) REVERT: B 12 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7843 (pp20) REVERT: B 13 GLN cc_start: 0.8760 (mm110) cc_final: 0.8409 (mm-40) REVERT: B 25 CYS cc_start: 0.8434 (m) cc_final: 0.8103 (p) REVERT: B 75 GLN cc_start: 0.8514 (mt0) cc_final: 0.7851 (mt0) REVERT: B 89 LYS cc_start: 0.8761 (mttp) cc_final: 0.8423 (mttp) REVERT: B 134 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7723 (mtm-85) REVERT: B 197 ARG cc_start: 0.8135 (mpt-90) cc_final: 0.7898 (tpp80) REVERT: B 215 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: B 219 ARG cc_start: 0.8439 (tpp80) cc_final: 0.8084 (mmt-90) REVERT: B 234 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: B 254 ASP cc_start: 0.7736 (t0) cc_final: 0.7530 (OUTLIER) REVERT: B 258 ASP cc_start: 0.8250 (t0) cc_final: 0.7306 (t0) REVERT: B 294 CYS cc_start: 0.8468 (m) cc_final: 0.8239 (t) REVERT: B 325 MET cc_start: 0.8592 (mmt) cc_final: 0.8362 (mmm) REVERT: G 18 GLN cc_start: 0.8741 (tp40) cc_final: 0.8074 (tp40) REVERT: G 42 GLU cc_start: 0.8500 (tt0) cc_final: 0.8298 (tt0) REVERT: N 35 ASN cc_start: 0.8960 (m-40) cc_final: 0.8727 (m-40) REVERT: N 90 ASP cc_start: 0.8790 (m-30) cc_final: 0.8586 (m-30) outliers start: 40 outliers final: 23 residues processed: 300 average time/residue: 1.5743 time to fit residues: 496.9091 Evaluate side-chains 297 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 281 CYS 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 460 CYS 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 35 GLN 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 175 GLN Chi-restraints excluded: chain B residue 215 GLU 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 25 ILE Chi-restraints excluded: chain N residue 25 SER 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 74 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 N 31 ASN N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085513 restraints weight = 18371.117| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.72 r_work: 0.3112 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9389 Z= 0.288 Angle : 0.637 9.445 12708 Z= 0.331 Chirality : 0.044 0.203 1405 Planarity : 0.005 0.052 1617 Dihedral : 4.542 47.144 1260 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.65 % Allowed : 24.42 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1123 helix: 2.16 (0.25), residues: 451 sheet: 0.44 (0.33), residues: 241 loop : -0.58 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 164 HIS 0.003 0.001 HIS P 32 PHE 0.014 0.001 PHE B 151 TYR 0.024 0.002 TYR N 60 ARG 0.009 0.001 ARG B 96 *********************** 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 320 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8469 (tp30) cc_final: 0.7905 (tp30) REVERT: R 37 GLN cc_start: 0.8919 (tp40) cc_final: 0.8495 (tp-100) REVERT: R 39 PHE cc_start: 0.9002 (t80) cc_final: 0.8702 (t80) REVERT: R 40 LEU cc_start: 0.9370 (mm) cc_final: 0.9134 (tp) REVERT: R 137 ASP cc_start: 0.7812 (m-30) cc_final: 0.7301 (m-30) REVERT: R 156 LEU cc_start: 0.7463 (mt) cc_final: 0.6783 (tt) REVERT: R 182 GLU cc_start: 0.7658 (tp30) cc_final: 0.7191 (tp30) REVERT: R 213 ARG cc_start: 0.7950 (tpt-90) cc_final: 0.7707 (tpt-90) REVERT: R 281 CYS cc_start: 0.6060 (OUTLIER) cc_final: 0.5767 (t) REVERT: R 407 LEU cc_start: 0.8358 (tp) cc_final: 0.8117 (tt) REVERT: R 425 MET cc_start: 0.8786 (ptm) cc_final: 0.8460 (ptm) REVERT: P 21 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.8283 (tpp80) REVERT: A 17 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8183 (mmtm) REVERT: A 27 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 29 GLN cc_start: 0.8423 (tp-100) cc_final: 0.7995 (tm-30) REVERT: A 38 ARG cc_start: 0.8377 (mtm110) cc_final: 0.8150 (mtm110) REVERT: A 223 ASP cc_start: 0.8191 (t0) cc_final: 0.7940 (t0) REVERT: A 347 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8060 (ttm-80) REVERT: A 381 ASP cc_start: 0.8576 (t0) cc_final: 0.8308 (t0) REVERT: B 12 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7769 (pp20) REVERT: B 25 CYS cc_start: 0.8418 (m) cc_final: 0.8101 (p) REVERT: B 89 LYS cc_start: 0.8786 (mttp) cc_final: 0.8475 (mttp) REVERT: B 172 GLU cc_start: 0.8479 (tp30) cc_final: 0.8154 (tp30) REVERT: B 175 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8350 (mp10) REVERT: B 197 ARG cc_start: 0.8127 (mpt-90) cc_final: 0.7620 (tpp80) REVERT: B 214 ARG cc_start: 0.8015 (ptp90) cc_final: 0.6399 (ptp90) REVERT: B 215 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: B 234 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: B 254 ASP cc_start: 0.7922 (t0) cc_final: 0.7703 (OUTLIER) REVERT: B 258 ASP cc_start: 0.8262 (t0) cc_final: 0.7348 (t0) REVERT: B 275 SER cc_start: 0.9014 (p) cc_final: 0.8809 (p) REVERT: B 294 CYS cc_start: 0.8521 (m) cc_final: 0.8284 (t) REVERT: B 325 MET cc_start: 0.8754 (mmt) cc_final: 0.8522 (mmm) REVERT: G 42 GLU cc_start: 0.8513 (tt0) cc_final: 0.8304 (tt0) outliers start: 36 outliers final: 18 residues processed: 297 average time/residue: 1.5785 time to fit residues: 492.9369 Evaluate side-chains 299 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 277 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 281 CYS 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 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 215 GLU 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 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 17 GLN N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.099537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084006 restraints weight = 18542.744| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.68 r_work: 0.3097 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9389 Z= 0.352 Angle : 0.684 10.136 12708 Z= 0.352 Chirality : 0.045 0.218 1405 Planarity : 0.005 0.056 1617 Dihedral : 4.668 48.194 1260 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.14 % Allowed : 25.43 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1123 helix: 2.07 (0.25), residues: 449 sheet: 0.25 (0.33), residues: 252 loop : -0.56 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 164 HIS 0.003 0.001 HIS P 32 PHE 0.016 0.002 PHE B 151 TYR 0.025 0.002 TYR N 60 ARG 0.009 0.001 ARG B 96 *********************** 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 316 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8498 (tp30) cc_final: 0.7942 (tp30) REVERT: R 37 GLN cc_start: 0.8987 (tp40) cc_final: 0.8530 (tp-100) REVERT: R 39 PHE cc_start: 0.9024 (t80) cc_final: 0.8728 (t80) REVERT: R 40 LEU cc_start: 0.9371 (mm) cc_final: 0.9128 (tp) REVERT: R 137 ASP cc_start: 0.7791 (m-30) cc_final: 0.7357 (m-30) REVERT: R 156 LEU cc_start: 0.7351 (mt) cc_final: 0.6654 (tt) REVERT: R 182 GLU cc_start: 0.7730 (tp30) cc_final: 0.7294 (tp30) REVERT: R 213 ARG cc_start: 0.7988 (tpt-90) cc_final: 0.7718 (tpt-90) REVERT: R 281 CYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5913 (t) REVERT: R 407 LEU cc_start: 0.8381 (tp) cc_final: 0.8137 (tt) REVERT: R 425 MET cc_start: 0.8820 (ptm) cc_final: 0.8505 (ptm) REVERT: R 463 ASN cc_start: 0.8136 (t0) cc_final: 0.7758 (t0) REVERT: R 469 GLU cc_start: 0.8260 (tp30) cc_final: 0.7692 (tp30) REVERT: P 21 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8252 (tpp80) REVERT: A 17 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8234 (mmtm) REVERT: A 27 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: A 29 GLN cc_start: 0.8491 (tp-100) cc_final: 0.8087 (tm-30) REVERT: A 38 ARG cc_start: 0.8386 (mtm110) cc_final: 0.8170 (mtm110) REVERT: A 223 ASP cc_start: 0.8178 (t0) cc_final: 0.7938 (t0) REVERT: A 295 ASP cc_start: 0.7959 (p0) cc_final: 0.7550 (p0) REVERT: A 381 ASP cc_start: 0.8605 (t0) cc_final: 0.8323 (t0) REVERT: B 12 GLU cc_start: 0.8231 (tm-30) cc_final: 0.8022 (pp20) REVERT: B 13 GLN cc_start: 0.8855 (mm110) cc_final: 0.8556 (mm-40) REVERT: B 25 CYS cc_start: 0.8425 (m) cc_final: 0.8110 (p) REVERT: B 89 LYS cc_start: 0.8801 (mttp) cc_final: 0.8504 (mttp) REVERT: B 172 GLU cc_start: 0.8463 (tp30) cc_final: 0.8066 (tp30) REVERT: B 197 ARG cc_start: 0.8175 (mpt-90) cc_final: 0.7659 (tpp80) REVERT: B 214 ARG cc_start: 0.8010 (ptp90) cc_final: 0.6432 (ptp90) REVERT: B 215 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: B 234 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: B 254 ASP cc_start: 0.7954 (t0) cc_final: 0.7741 (OUTLIER) REVERT: B 258 ASP cc_start: 0.8278 (t0) cc_final: 0.7360 (t0) REVERT: B 275 SER cc_start: 0.9021 (p) cc_final: 0.8799 (p) REVERT: B 294 CYS cc_start: 0.8588 (m) cc_final: 0.8311 (t) REVERT: G 20 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8790 (ttpt) REVERT: G 42 GLU cc_start: 0.8474 (tt0) cc_final: 0.8261 (tt0) REVERT: N 13 GLN cc_start: 0.8358 (pp30) cc_final: 0.8092 (mm-40) REVERT: N 35 ASN cc_start: 0.9096 (m-40) cc_final: 0.8750 (m-40) REVERT: N 53 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7685 (mp-120) REVERT: N 115 TYR cc_start: 0.8959 (t80) cc_final: 0.8590 (t80) outliers start: 31 outliers final: 20 residues processed: 297 average time/residue: 1.5086 time to fit residues: 471.2156 Evaluate side-chains 302 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 278 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 281 CYS 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 35 GLN 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 215 GLU 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 N residue 25 SER Chi-restraints excluded: chain N residue 53 GLN 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 43 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS B 75 GLN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086630 restraints weight = 18279.679| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.66 r_work: 0.3144 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9389 Z= 0.211 Angle : 0.678 10.900 12708 Z= 0.345 Chirality : 0.044 0.244 1405 Planarity : 0.004 0.050 1617 Dihedral : 4.449 44.299 1260 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.53 % Allowed : 27.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1123 helix: 2.19 (0.25), residues: 443 sheet: 0.47 (0.33), residues: 238 loop : -0.55 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 164 HIS 0.003 0.001 HIS R 42 PHE 0.014 0.001 PHE A 212 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.001 ARG B 19 *********************** 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 299 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8462 (tp30) cc_final: 0.7896 (tp30) REVERT: R 37 GLN cc_start: 0.8926 (tp40) cc_final: 0.8506 (tp-100) REVERT: R 39 PHE cc_start: 0.8973 (t80) cc_final: 0.8406 (t80) REVERT: R 40 LEU cc_start: 0.9368 (mm) cc_final: 0.9123 (tp) REVERT: R 137 ASP cc_start: 0.7728 (m-30) cc_final: 0.7120 (m-30) REVERT: R 182 GLU cc_start: 0.7575 (tp30) cc_final: 0.7113 (tp30) REVERT: R 213 ARG cc_start: 0.7883 (tpt-90) cc_final: 0.7637 (tpt-90) REVERT: R 281 CYS cc_start: 0.6003 (OUTLIER) cc_final: 0.5747 (t) REVERT: R 407 LEU cc_start: 0.8388 (tp) cc_final: 0.8157 (tt) REVERT: R 425 MET cc_start: 0.8786 (ptm) cc_final: 0.8483 (ptm) REVERT: R 469 GLU cc_start: 0.8199 (tp30) cc_final: 0.7615 (tp30) REVERT: P 21 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8243 (tpp80) REVERT: A 27 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 29 GLN cc_start: 0.8497 (tp-100) cc_final: 0.8100 (tm-30) REVERT: A 38 ARG cc_start: 0.8365 (mtm110) cc_final: 0.8158 (mtm110) REVERT: A 347 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.8124 (ttm-80) REVERT: A 381 ASP cc_start: 0.8585 (t0) cc_final: 0.8274 (t0) REVERT: B 12 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7901 (pp20) REVERT: B 25 CYS cc_start: 0.8423 (m) cc_final: 0.8146 (p) REVERT: B 89 LYS cc_start: 0.8823 (mttp) cc_final: 0.8546 (mttp) REVERT: B 172 GLU cc_start: 0.8503 (tp30) cc_final: 0.8125 (tp30) REVERT: B 197 ARG cc_start: 0.8138 (mpt-90) cc_final: 0.7648 (tpp80) REVERT: B 214 ARG cc_start: 0.8006 (ptp90) cc_final: 0.6485 (ptp90) REVERT: B 234 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: B 258 ASP cc_start: 0.8288 (t0) cc_final: 0.7399 (t0) REVERT: B 294 CYS cc_start: 0.8538 (m) cc_final: 0.8210 (t) REVERT: B 325 MET cc_start: 0.8646 (mmt) cc_final: 0.8439 (mmm) REVERT: G 42 GLU cc_start: 0.8482 (tt0) cc_final: 0.8273 (tt0) REVERT: N 13 GLN cc_start: 0.8296 (pp30) cc_final: 0.8086 (mm-40) REVERT: N 35 ASN cc_start: 0.9002 (m-40) cc_final: 0.8745 (m-40) REVERT: N 115 TYR cc_start: 0.8926 (t80) cc_final: 0.8615 (t80) outliers start: 25 outliers final: 15 residues processed: 284 average time/residue: 1.7207 time to fit residues: 513.2602 Evaluate side-chains 289 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 271 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 CYS 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 35 GLN 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 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 N residue 25 SER 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: 0.6980 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 R 358 ASN A 357 HIS G 18 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 = 0.3549 r_free = 0.3549 target = 0.101258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.085817 restraints weight = 18396.816| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.68 r_work: 0.3127 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9389 Z= 0.252 Angle : 0.699 10.627 12708 Z= 0.354 Chirality : 0.045 0.220 1405 Planarity : 0.004 0.058 1617 Dihedral : 4.505 45.142 1260 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.33 % Allowed : 26.75 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1123 helix: 2.12 (0.25), residues: 443 sheet: 0.38 (0.33), residues: 240 loop : -0.55 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 164 HIS 0.008 0.001 HIS R 42 PHE 0.014 0.001 PHE A 212 TYR 0.024 0.001 TYR R 191 ARG 0.012 0.001 ARG B 8 ********************** 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 296 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 273 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8451 (tp30) cc_final: 0.7869 (tp30) REVERT: R 37 GLN cc_start: 0.8959 (tp40) cc_final: 0.8510 (tp-100) REVERT: R 39 PHE cc_start: 0.8893 (t80) cc_final: 0.8534 (t80) REVERT: R 40 LEU cc_start: 0.9352 (mm) cc_final: 0.9150 (tp) REVERT: R 42 HIS cc_start: 0.8451 (p-80) cc_final: 0.8211 (p90) REVERT: R 137 ASP cc_start: 0.7761 (m-30) cc_final: 0.7123 (m-30) REVERT: R 156 LEU cc_start: 0.7103 (mt) cc_final: 0.6444 (tt) REVERT: R 169 GLU cc_start: 0.8846 (tt0) cc_final: 0.8624 (tm-30) REVERT: R 182 GLU cc_start: 0.7614 (tp30) cc_final: 0.7162 (tp30) REVERT: R 213 ARG cc_start: 0.7913 (tpt-90) cc_final: 0.7651 (tpt-90) REVERT: R 281 CYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5783 (t) REVERT: R 407 LEU cc_start: 0.8388 (tp) cc_final: 0.8157 (tt) REVERT: R 425 MET cc_start: 0.8787 (ptm) cc_final: 0.8481 (ptm) REVERT: R 463 ASN cc_start: 0.8088 (t0) cc_final: 0.7744 (t0) REVERT: R 469 GLU cc_start: 0.8239 (tp30) cc_final: 0.7663 (tp30) REVERT: P 21 ARG cc_start: 0.8627 (ttm-80) cc_final: 0.8256 (tpp80) REVERT: A 27 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 29 GLN cc_start: 0.8507 (tp-100) cc_final: 0.8119 (tm-30) REVERT: A 38 ARG cc_start: 0.8341 (mtm110) cc_final: 0.8106 (mtm110) REVERT: A 240 ASP cc_start: 0.7979 (p0) cc_final: 0.7771 (p0) REVERT: A 347 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8162 (ttm-80) REVERT: A 381 ASP cc_start: 0.8592 (t0) cc_final: 0.8309 (t0) REVERT: B 13 GLN cc_start: 0.8746 (mm110) cc_final: 0.8471 (mm-40) REVERT: B 25 CYS cc_start: 0.8381 (m) cc_final: 0.8124 (p) REVERT: B 89 LYS cc_start: 0.8826 (mttp) cc_final: 0.8537 (mttp) REVERT: B 172 GLU cc_start: 0.8511 (tp30) cc_final: 0.8113 (tp30) REVERT: B 197 ARG cc_start: 0.8174 (mpt-90) cc_final: 0.7869 (tpp80) REVERT: B 234 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: B 258 ASP cc_start: 0.8285 (t0) cc_final: 0.7389 (t0) REVERT: B 275 SER cc_start: 0.9034 (p) cc_final: 0.8812 (p) REVERT: B 294 CYS cc_start: 0.8584 (m) cc_final: 0.8253 (t) REVERT: B 325 MET cc_start: 0.8706 (mmt) cc_final: 0.8497 (mmm) REVERT: N 13 GLN cc_start: 0.8301 (pp30) cc_final: 0.8069 (mm-40) outliers start: 23 outliers final: 18 residues processed: 283 average time/residue: 2.0273 time to fit residues: 602.5900 Evaluate side-chains 296 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 275 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 281 CYS 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 35 GLN 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 118 ASP 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 N residue 25 SER 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 16 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 R 440 GLN A 357 HIS B 75 GLN G 18 GLN N 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.102259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086678 restraints weight = 18341.687| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.69 r_work: 0.3148 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9389 Z= 0.200 Angle : 0.693 10.355 12708 Z= 0.351 Chirality : 0.044 0.214 1405 Planarity : 0.005 0.058 1617 Dihedral : 4.446 44.018 1260 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.23 % Allowed : 27.05 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1123 helix: 2.15 (0.25), residues: 443 sheet: 0.41 (0.33), residues: 240 loop : -0.51 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP R 164 HIS 0.009 0.001 HIS R 42 PHE 0.014 0.001 PHE A 212 TYR 0.024 0.001 TYR R 191 ARG 0.016 0.001 ARG R 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9573.15 seconds wall clock time: 169 minutes 1.41 seconds (10141.41 seconds total)