Starting phenix.real_space_refine on Mon May 12 17:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y35_33588/05_2025/7y35_33588.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y35_33588/05_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_33588/05_2025/7y35_33588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y35_33588/05_2025/7y35_33588.map" model { file = "/net/cci-nas-00/data/ceres_data/7y35_33588/05_2025/7y35_33588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y35_33588/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.60, per 1000 atoms: 0.61 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 2.90 Time building geometry restraints manager: 2.86 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: 1.510 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.020 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.104 9396 Z= 0.426 Angle : 0.802 17.243 12720 Z= 0.480 Chirality : 0.052 0.202 1405 Planarity : 0.005 0.076 1617 Dihedral : 12.994 84.106 3394 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 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 Details of bonding type rmsd hydrogen bonds : bond 0.17052 ( 464) hydrogen bonds : angle 6.54788 ( 1344) SS BOND : bond 0.00937 ( 6) SS BOND : angle 3.49735 ( 12) covalent geometry : bond 0.00903 ( 9389) covalent geometry : angle 0.79509 (12708) Misc. bond : bond 0.10398 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 0.961 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: 1.4624 time to fit residues: 531.1274 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 : 1.070 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.106296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.090338 restraints weight = 17833.623| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.67 r_work: 0.3217 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 9396 Z= 0.142 Angle : 0.610 7.618 12720 Z= 0.324 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 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 464) hydrogen bonds : angle 4.63976 ( 1344) SS BOND : bond 0.00599 ( 6) SS BOND : angle 1.78064 ( 12) covalent geometry : bond 0.00308 ( 9389) covalent geometry : angle 0.60769 (12708) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 GLN cc_start: 0.8746 (tp40) cc_final: 0.8433 (tp40) REVERT: R 39 PHE cc_start: 0.9008 (t80) cc_final: 0.8650 (t80) REVERT: R 43 ARG cc_start: 0.8519 (mmm160) cc_final: 0.8244 (mmm160) REVERT: R 156 LEU cc_start: 0.7264 (mt) cc_final: 0.6832 (tt) REVERT: R 160 HIS cc_start: 0.7385 (m90) cc_final: 0.6990 (m90) REVERT: R 182 GLU cc_start: 0.7397 (tp30) cc_final: 0.7042 (tp30) REVERT: R 207 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8371 (mm) REVERT: R 346 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8599 (mt) REVERT: R 407 LEU cc_start: 0.8287 (tp) cc_final: 0.7976 (tt) REVERT: R 425 MET cc_start: 0.8729 (ptm) cc_final: 0.8528 (ptm) REVERT: P 27 LEU cc_start: 0.8829 (mm) cc_final: 0.8586 (mm) REVERT: A 17 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7962 (mmtm) REVERT: A 27 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: A 34 LYS cc_start: 0.8992 (tttt) cc_final: 0.8667 (ttmm) REVERT: A 38 ARG cc_start: 0.8336 (mtm110) cc_final: 0.8055 (mtm110) REVERT: A 46 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 53 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8143 (ttpp) REVERT: A 54 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8816 (t) REVERT: A 240 ASP cc_start: 0.7615 (m-30) cc_final: 0.7381 (m-30) REVERT: A 280 LYS cc_start: 0.8836 (ttpp) cc_final: 0.8628 (ttpp) REVERT: A 311 TYR cc_start: 0.8419 (m-80) cc_final: 0.8119 (m-80) REVERT: A 343 ASP cc_start: 0.8663 (m-30) cc_final: 0.8368 (m-30) REVERT: B 12 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7874 (pp20) REVERT: B 22 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7517 (mtm-85) REVERT: B 25 CYS cc_start: 0.8440 (m) cc_final: 0.7937 (p) REVERT: B 32 GLN cc_start: 0.8402 (mt0) cc_final: 0.8085 (mt0) REVERT: B 46 ARG cc_start: 0.8501 (mtp180) cc_final: 0.7987 (ttm110) REVERT: B 75 GLN cc_start: 0.8697 (mt0) cc_final: 0.8407 (mt0) REVERT: B 89 LYS cc_start: 0.8800 (mttp) cc_final: 0.8385 (mttp) REVERT: B 134 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7603 (mtm-85) REVERT: B 214 ARG cc_start: 0.8144 (ptp90) cc_final: 0.7678 (ptp90) REVERT: B 215 GLU cc_start: 0.8228 (mp0) cc_final: 0.7929 (mp0) REVERT: B 258 ASP cc_start: 0.8264 (t0) cc_final: 0.6893 (t0) REVERT: B 294 CYS cc_start: 0.8520 (m) cc_final: 0.8268 (t) REVERT: G 42 GLU cc_start: 0.8504 (tt0) cc_final: 0.8281 (tt0) REVERT: N 69 THR cc_start: 0.8818 (m) cc_final: 0.8433 (p) REVERT: N 78 THR cc_start: 0.9033 (t) cc_final: 0.8752 (p) outliers start: 34 outliers final: 17 residues processed: 311 average time/residue: 1.4092 time to fit residues: 462.3309 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 : 1.045 ------------------------------------------------------------------------------- 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: 0.4980 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 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: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.106130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089951 restraints weight = 18247.099| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.73 r_work: 0.3201 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 0.031 9396 Z= 0.125 Angle : 0.584 8.798 12720 Z= 0.306 Chirality : 0.042 0.236 1405 Planarity : 0.004 0.054 1617 Dihedral : 4.547 45.362 1260 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.95 % Allowed : 18.95 % 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: 0.44 (0.25), residues: 1123 helix: 1.63 (0.25), residues: 455 sheet: 0.04 (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 0.011 0.001 ARG R 150 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 464) hydrogen bonds : angle 4.31546 ( 1344) SS BOND : bond 0.00375 ( 6) SS BOND : angle 1.44626 ( 12) covalent geometry : bond 0.00273 ( 9389) covalent geometry : angle 0.58293 (12708) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 291 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8459 (tp30) cc_final: 0.7802 (tp30) REVERT: R 37 GLN cc_start: 0.8795 (tp40) cc_final: 0.8444 (tp40) REVERT: R 39 PHE cc_start: 0.9013 (t80) cc_final: 0.8659 (t80) REVERT: R 40 LEU cc_start: 0.9365 (mm) cc_final: 0.8870 (mm) REVERT: R 156 LEU cc_start: 0.7232 (mt) cc_final: 0.6678 (tt) REVERT: R 160 HIS cc_start: 0.7543 (m90) cc_final: 0.7200 (m90) REVERT: R 182 GLU cc_start: 0.7394 (tp30) cc_final: 0.6987 (tp30) REVERT: R 207 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8392 (mm) REVERT: R 346 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8645 (mt) REVERT: R 407 LEU cc_start: 0.8291 (tp) cc_final: 0.8003 (tt) REVERT: R 425 MET cc_start: 0.8703 (ptm) cc_final: 0.8290 (ptm) REVERT: A 17 LYS cc_start: 0.8343 (mmtm) cc_final: 0.8076 (mmtm) REVERT: A 27 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 34 LYS cc_start: 0.8962 (tttt) cc_final: 0.8685 (ttmm) REVERT: A 38 ARG cc_start: 0.8320 (mtm110) cc_final: 0.8062 (mtm110) REVERT: A 46 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 227 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8466 (mm-40) REVERT: A 311 TYR cc_start: 0.8445 (m-80) cc_final: 0.8228 (m-80) REVERT: A 333 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7676 (mtm-85) REVERT: A 343 ASP cc_start: 0.8641 (m-30) cc_final: 0.8310 (m-30) REVERT: B 22 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7599 (mtm-85) REVERT: B 25 CYS cc_start: 0.8429 (m) cc_final: 0.8023 (p) REVERT: B 32 GLN cc_start: 0.8354 (mt0) cc_final: 0.7991 (mt0) REVERT: B 57 LYS cc_start: 0.9108 (mtmm) cc_final: 0.8847 (ptmt) REVERT: B 89 LYS cc_start: 0.8786 (mttp) cc_final: 0.8494 (mttp) REVERT: B 134 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7609 (mtm-85) REVERT: B 214 ARG cc_start: 0.8086 (ptp90) cc_final: 0.7641 (ptp90) REVERT: B 215 GLU cc_start: 0.8248 (mp0) cc_final: 0.8019 (mp0) REVERT: B 217 MET cc_start: 0.8308 (pp-130) cc_final: 0.8033 (ppp) REVERT: B 234 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: B 258 ASP cc_start: 0.8204 (t0) cc_final: 0.6813 (t0) REVERT: B 275 SER cc_start: 0.8912 (m) cc_final: 0.8711 (p) REVERT: B 294 CYS cc_start: 0.8552 (m) cc_final: 0.8322 (t) REVERT: G 42 GLU cc_start: 0.8530 (tt0) cc_final: 0.8305 (tt0) REVERT: N 35 ASN cc_start: 0.8959 (m-40) cc_final: 0.8672 (m-40) REVERT: N 69 THR cc_start: 0.8847 (m) cc_final: 0.8477 (p) REVERT: N 78 THR cc_start: 0.9151 (t) cc_final: 0.8839 (p) outliers start: 39 outliers final: 20 residues processed: 307 average time/residue: 1.4130 time to fit residues: 457.7686 Evaluate side-chains 308 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 R residue 472 LYS 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 207 ILE Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 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: 0.6980 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 75 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088926 restraints weight = 18115.126| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.70 r_work: 0.3182 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9396 Z= 0.135 Angle : 0.585 8.707 12720 Z= 0.306 Chirality : 0.042 0.196 1405 Planarity : 0.004 0.051 1617 Dihedral : 4.420 45.153 1260 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.26 % Allowed : 20.36 % Favored : 75.38 % 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: 0.85 (0.26), residues: 1123 helix: 1.98 (0.26), residues: 450 sheet: 0.27 (0.34), residues: 239 loop : -0.75 (0.30), 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 0.012 0.001 PHE B 241 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.001 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 464) hydrogen bonds : angle 4.17429 ( 1344) SS BOND : bond 0.00158 ( 6) SS BOND : angle 1.21261 ( 12) covalent geometry : bond 0.00305 ( 9389) covalent geometry : angle 0.58433 (12708) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 1.031 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: 0.8478 (tp30) cc_final: 0.7949 (tp30) REVERT: R 37 GLN cc_start: 0.8852 (tp40) cc_final: 0.8400 (tp-100) REVERT: R 39 PHE cc_start: 0.9015 (t80) cc_final: 0.8684 (t80) REVERT: R 40 LEU cc_start: 0.9362 (mm) cc_final: 0.9097 (tp) REVERT: R 137 ASP cc_start: 0.7738 (m-30) cc_final: 0.7081 (m-30) REVERT: R 156 LEU cc_start: 0.7278 (mt) cc_final: 0.6669 (tt) REVERT: R 160 HIS cc_start: 0.7517 (m90) cc_final: 0.7207 (m90) REVERT: R 182 GLU cc_start: 0.7541 (tp30) cc_final: 0.7113 (tp30) REVERT: R 207 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8334 (mm) REVERT: R 407 LEU cc_start: 0.8308 (tp) cc_final: 0.8052 (tt) REVERT: R 425 MET cc_start: 0.8753 (ptm) cc_final: 0.8367 (ptm) REVERT: P 21 ARG cc_start: 0.8678 (ttm-80) cc_final: 0.8389 (tpp80) REVERT: P 26 LYS cc_start: 0.8815 (tmmt) cc_final: 0.8517 (tmmt) REVERT: A 17 LYS cc_start: 0.8373 (mmtm) cc_final: 0.8158 (mmtm) REVERT: A 27 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: A 34 LYS cc_start: 0.8965 (tttt) cc_final: 0.8676 (ttmm) REVERT: A 38 ARG cc_start: 0.8346 (mtm110) cc_final: 0.8095 (mtm110) REVERT: A 46 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8043 (tt) REVERT: B 5 ASP cc_start: 0.8123 (p0) cc_final: 0.7730 (p0) REVERT: B 12 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7821 (pp20) REVERT: B 22 ARG cc_start: 0.8240 (mtt180) cc_final: 0.7604 (mtm-85) REVERT: B 25 CYS cc_start: 0.8385 (m) cc_final: 0.8043 (p) REVERT: B 32 GLN cc_start: 0.8328 (mt0) cc_final: 0.7983 (mt0) REVERT: B 57 LYS cc_start: 0.9111 (mtmm) cc_final: 0.8906 (pttt) REVERT: B 89 LYS cc_start: 0.8781 (mttp) cc_final: 0.8458 (mttp) REVERT: B 134 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7658 (mtm-85) REVERT: B 197 ARG cc_start: 0.8100 (mpt-90) cc_final: 0.7886 (tpp80) REVERT: B 234 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: B 254 ASP cc_start: 0.7856 (t0) cc_final: 0.7598 (t0) REVERT: B 258 ASP cc_start: 0.8205 (t0) cc_final: 0.6802 (t0) REVERT: B 275 SER cc_start: 0.8929 (m) cc_final: 0.8669 (p) REVERT: B 294 CYS cc_start: 0.8539 (m) cc_final: 0.8298 (t) REVERT: G 18 GLN cc_start: 0.8721 (tp40) cc_final: 0.8055 (tp40) REVERT: G 42 GLU cc_start: 0.8528 (tt0) cc_final: 0.8299 (tt0) REVERT: N 25 SER cc_start: 0.8482 (OUTLIER) cc_final: 0.8275 (p) REVERT: N 35 ASN cc_start: 0.8976 (m-40) cc_final: 0.8724 (m-40) REVERT: N 69 THR cc_start: 0.8891 (m) cc_final: 0.8561 (p) REVERT: N 78 THR cc_start: 0.9199 (t) cc_final: 0.8832 (p) REVERT: N 95 TYR cc_start: 0.8982 (m-80) cc_final: 0.8348 (m-80) REVERT: N 114 THR cc_start: 0.8940 (t) cc_final: 0.8615 (p) outliers start: 42 outliers final: 21 residues processed: 304 average time/residue: 1.4174 time to fit residues: 454.4645 Evaluate side-chains 313 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 287 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 404 ARG 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 325 THR 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 Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 77 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 0.0070 chunk 6 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- 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 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 = 0.3610 r_free = 0.3610 target = 0.105274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088894 restraints weight = 18071.775| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.71 r_work: 0.3180 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9396 Z= 0.120 Angle : 0.577 8.833 12720 Z= 0.301 Chirality : 0.042 0.190 1405 Planarity : 0.004 0.051 1617 Dihedral : 4.289 43.805 1260 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.65 % Allowed : 21.38 % Favored : 74.97 % 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: 1.13 (0.26), residues: 1123 helix: 2.22 (0.26), residues: 444 sheet: 0.35 (0.34), residues: 243 loop : -0.55 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 164 HIS 0.002 0.000 HIS R 114 PHE 0.011 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 464) hydrogen bonds : angle 4.05429 ( 1344) SS BOND : bond 0.00137 ( 6) SS BOND : angle 0.98048 ( 12) covalent geometry : bond 0.00267 ( 9389) covalent geometry : angle 0.57608 (12708) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8431 (tp30) cc_final: 0.7858 (tp30) REVERT: R 37 GLN cc_start: 0.8810 (tp40) cc_final: 0.8417 (tp-100) REVERT: R 39 PHE cc_start: 0.8980 (t80) cc_final: 0.8621 (t80) REVERT: R 40 LEU cc_start: 0.9350 (mm) cc_final: 0.9122 (tp) REVERT: R 137 ASP cc_start: 0.7840 (m-30) cc_final: 0.7025 (m-30) REVERT: R 156 LEU cc_start: 0.7308 (mt) cc_final: 0.6727 (tt) REVERT: R 160 HIS cc_start: 0.7515 (m90) cc_final: 0.7213 (m90) REVERT: R 182 GLU cc_start: 0.7514 (tp30) cc_final: 0.7089 (tp30) REVERT: R 356 SER cc_start: 0.7704 (t) cc_final: 0.7384 (p) REVERT: R 407 LEU cc_start: 0.8301 (tp) cc_final: 0.8063 (tt) REVERT: R 425 MET cc_start: 0.8712 (ptm) cc_final: 0.8347 (ptm) REVERT: R 431 GLU cc_start: 0.7537 (tp30) cc_final: 0.7305 (tp30) REVERT: P 21 ARG cc_start: 0.8665 (ttm-80) cc_final: 0.8390 (tpp80) REVERT: A 27 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: A 34 LYS cc_start: 0.8972 (tttt) cc_final: 0.8633 (ttpp) REVERT: A 38 ARG cc_start: 0.8362 (mtm110) cc_final: 0.8122 (mtm110) REVERT: A 46 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7870 (tt) REVERT: A 223 ASP cc_start: 0.8172 (t0) cc_final: 0.7942 (t0) REVERT: A 311 TYR cc_start: 0.8460 (m-80) cc_final: 0.8223 (m-80) REVERT: A 381 ASP cc_start: 0.8527 (t0) cc_final: 0.8299 (t0) REVERT: B 12 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7831 (pp20) REVERT: B 22 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7882 (mtm180) REVERT: B 25 CYS cc_start: 0.8430 (m) cc_final: 0.8099 (p) REVERT: B 59 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.8689 (m-80) REVERT: B 89 LYS cc_start: 0.8775 (mttp) cc_final: 0.8451 (mttp) REVERT: B 127 LYS cc_start: 0.8869 (mmtp) cc_final: 0.8662 (mmtp) REVERT: B 134 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7697 (mtm-85) REVERT: B 175 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8384 (mp10) REVERT: B 215 GLU cc_start: 0.8297 (mp0) cc_final: 0.7689 (mp0) REVERT: B 234 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: B 254 ASP cc_start: 0.7814 (t0) cc_final: 0.7476 (t0) REVERT: B 258 ASP cc_start: 0.8179 (t0) cc_final: 0.7246 (t0) REVERT: B 318 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8826 (mt) REVERT: G 18 GLN cc_start: 0.8710 (tp40) cc_final: 0.8038 (tp40) REVERT: G 42 GLU cc_start: 0.8493 (tt0) cc_final: 0.8278 (tt0) REVERT: N 35 ASN cc_start: 0.8942 (m-40) cc_final: 0.8721 (m-40) REVERT: N 69 THR cc_start: 0.8906 (m) cc_final: 0.8582 (p) REVERT: N 78 THR cc_start: 0.9148 (t) cc_final: 0.8769 (p) REVERT: N 95 TYR cc_start: 0.8999 (m-80) cc_final: 0.8443 (m-80) outliers start: 36 outliers final: 19 residues processed: 302 average time/residue: 1.3962 time to fit residues: 444.9133 Evaluate side-chains 302 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 277 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 404 ARG Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN 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 B residue 318 LEU 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: 3.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 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 = 0.3584 r_free = 0.3584 target = 0.103609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087315 restraints weight = 18066.105| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.70 r_work: 0.3152 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9396 Z= 0.149 Angle : 0.614 9.711 12720 Z= 0.315 Chirality : 0.043 0.200 1405 Planarity : 0.004 0.052 1617 Dihedral : 4.347 44.814 1260 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.15 % Allowed : 22.70 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.26), residues: 1123 helix: 2.27 (0.25), residues: 444 sheet: 0.51 (0.34), residues: 239 loop : -0.52 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 164 HIS 0.002 0.001 HIS P 32 PHE 0.012 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.011 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 464) hydrogen bonds : angle 4.06415 ( 1344) SS BOND : bond 0.00165 ( 6) SS BOND : angle 1.03828 ( 12) covalent geometry : bond 0.00347 ( 9389) covalent geometry : angle 0.61384 (12708) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8409 (tp30) cc_final: 0.7910 (tp30) REVERT: R 37 GLN cc_start: 0.8818 (tp40) cc_final: 0.8396 (tp-100) REVERT: R 39 PHE cc_start: 0.8974 (t80) cc_final: 0.8640 (t80) REVERT: R 40 LEU cc_start: 0.9340 (mm) cc_final: 0.9119 (tp) REVERT: R 137 ASP cc_start: 0.7914 (m-30) cc_final: 0.7152 (m-30) REVERT: R 154 TRP cc_start: 0.6995 (m100) cc_final: 0.6756 (m100) REVERT: R 156 LEU cc_start: 0.7379 (mt) cc_final: 0.6691 (tt) REVERT: R 182 GLU cc_start: 0.7546 (tp30) cc_final: 0.7081 (tp30) REVERT: R 281 CYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5682 (t) REVERT: R 407 LEU cc_start: 0.8346 (tp) cc_final: 0.8102 (tt) REVERT: R 414 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8482 (mmm) REVERT: R 425 MET cc_start: 0.8752 (ptm) cc_final: 0.8398 (ptm) REVERT: A 27 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: A 34 LYS cc_start: 0.9036 (tttt) cc_final: 0.8704 (ttpp) REVERT: A 38 ARG cc_start: 0.8323 (mtm110) cc_final: 0.8112 (mtm110) REVERT: A 55 THR cc_start: 0.8763 (m) cc_final: 0.8526 (p) REVERT: A 223 ASP cc_start: 0.8161 (t0) cc_final: 0.7902 (t0) REVERT: A 336 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7970 (ttt-90) REVERT: A 347 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8015 (ttm-80) REVERT: A 381 ASP cc_start: 0.8523 (t0) cc_final: 0.8250 (t0) REVERT: B 12 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7904 (pp20) REVERT: B 22 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8030 (mtm180) REVERT: B 25 CYS cc_start: 0.8440 (m) cc_final: 0.8116 (p) REVERT: B 59 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.8721 (m-80) REVERT: B 75 GLN cc_start: 0.8451 (mt0) cc_final: 0.7907 (mt0) REVERT: B 76 ASP cc_start: 0.8519 (p0) cc_final: 0.8068 (p0) REVERT: B 89 LYS cc_start: 0.8764 (mttp) cc_final: 0.8426 (mttp) REVERT: B 134 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7732 (mtm-85) REVERT: B 175 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: B 197 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7754 (tpp80) REVERT: B 214 ARG cc_start: 0.7944 (ptp90) cc_final: 0.7399 (ptp90) REVERT: B 215 GLU cc_start: 0.8339 (mp0) cc_final: 0.7844 (mp0) REVERT: B 219 ARG cc_start: 0.8461 (tpp80) cc_final: 0.8196 (mmt90) REVERT: B 234 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: B 254 ASP cc_start: 0.7878 (t0) cc_final: 0.7558 (t0) REVERT: B 258 ASP cc_start: 0.8252 (t0) cc_final: 0.7305 (t0) REVERT: B 325 MET cc_start: 0.8672 (mmt) cc_final: 0.8448 (mmm) REVERT: G 18 GLN cc_start: 0.8762 (tp40) cc_final: 0.7978 (tp40) REVERT: G 42 GLU cc_start: 0.8499 (tt0) cc_final: 0.8298 (tt0) REVERT: N 35 ASN cc_start: 0.8976 (m-40) cc_final: 0.8688 (m-40) REVERT: N 95 TYR cc_start: 0.9048 (m-80) cc_final: 0.8412 (m-80) outliers start: 41 outliers final: 22 residues processed: 300 average time/residue: 1.5938 time to fit residues: 503.3427 Evaluate side-chains 308 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 404 ARG Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 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 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN 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 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.103182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.087027 restraints weight = 18350.511| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.72 r_work: 0.3141 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9396 Z= 0.150 Angle : 0.628 11.075 12720 Z= 0.323 Chirality : 0.043 0.211 1405 Planarity : 0.004 0.053 1617 Dihedral : 4.415 44.882 1260 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.15 % Allowed : 23.71 % Favored : 72.14 % 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: 1.22 (0.26), residues: 1123 helix: 2.28 (0.25), residues: 444 sheet: 0.46 (0.34), residues: 239 loop : -0.51 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 164 HIS 0.004 0.001 HIS R 42 PHE 0.012 0.001 PHE B 151 TYR 0.024 0.001 TYR R 191 ARG 0.010 0.001 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 464) hydrogen bonds : angle 4.05727 ( 1344) SS BOND : bond 0.00181 ( 6) SS BOND : angle 1.00783 ( 12) covalent geometry : bond 0.00350 ( 9389) covalent geometry : angle 0.62714 (12708) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8442 (tp30) cc_final: 0.7886 (tp30) REVERT: R 37 GLN cc_start: 0.8869 (tp40) cc_final: 0.8465 (tp-100) REVERT: R 39 PHE cc_start: 0.8965 (t80) cc_final: 0.8683 (t80) REVERT: R 40 LEU cc_start: 0.9354 (mm) cc_final: 0.9128 (tp) REVERT: R 137 ASP cc_start: 0.7756 (m-30) cc_final: 0.7265 (m-30) REVERT: R 154 TRP cc_start: 0.7006 (m100) cc_final: 0.6793 (m100) REVERT: R 156 LEU cc_start: 0.7498 (mt) cc_final: 0.6811 (tt) REVERT: R 182 GLU cc_start: 0.7605 (tp30) cc_final: 0.7111 (tp30) REVERT: R 281 CYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5676 (t) REVERT: R 407 LEU cc_start: 0.8342 (tp) cc_final: 0.8102 (tt) REVERT: R 425 MET cc_start: 0.8777 (ptm) cc_final: 0.8423 (ptm) REVERT: R 469 GLU cc_start: 0.8168 (tp30) cc_final: 0.7569 (tp30) REVERT: P 21 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8247 (tpp80) REVERT: A 27 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: A 34 LYS cc_start: 0.9037 (tttt) cc_final: 0.8698 (ttpp) REVERT: A 38 ARG cc_start: 0.8343 (mtm110) cc_final: 0.8129 (mtm110) REVERT: A 336 ARG cc_start: 0.8226 (ttt-90) cc_final: 0.7986 (ttt-90) REVERT: A 347 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8048 (ttm-80) REVERT: B 22 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8117 (mtm180) REVERT: B 25 CYS cc_start: 0.8423 (m) cc_final: 0.8124 (p) REVERT: B 89 LYS cc_start: 0.8783 (mttp) cc_final: 0.8442 (mttp) REVERT: B 134 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7684 (mtm-85) REVERT: B 172 GLU cc_start: 0.8457 (tp30) cc_final: 0.8137 (tp30) REVERT: B 175 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8413 (mp10) REVERT: B 197 ARG cc_start: 0.8273 (tpp80) cc_final: 0.7648 (tpp80) REVERT: B 214 ARG cc_start: 0.7934 (ptp90) cc_final: 0.7352 (ptp90) REVERT: B 215 GLU cc_start: 0.8309 (mp0) cc_final: 0.7747 (mp0) REVERT: B 219 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8106 (mmt90) REVERT: B 234 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8111 (m-80) REVERT: B 254 ASP cc_start: 0.7879 (t0) cc_final: 0.7574 (t0) REVERT: B 258 ASP cc_start: 0.8267 (t0) cc_final: 0.7309 (t0) REVERT: B 325 MET cc_start: 0.8676 (mmt) cc_final: 0.8457 (mmm) REVERT: G 18 GLN cc_start: 0.8641 (tp40) cc_final: 0.8102 (tp40) REVERT: G 42 GLU cc_start: 0.8530 (tt0) cc_final: 0.8318 (tt0) REVERT: N 35 ASN cc_start: 0.8989 (m-40) cc_final: 0.8774 (m-40) outliers start: 41 outliers final: 23 residues processed: 296 average time/residue: 1.4560 time to fit residues: 453.6014 Evaluate side-chains 304 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU 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 404 ARG Chi-restraints excluded: chain R residue 411 LEU 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 299 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 175 GLN 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 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS R 223 HIS A 357 HIS A 384 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 = 0.3558 r_free = 0.3558 target = 0.101821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.086267 restraints weight = 18518.871| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.67 r_work: 0.3136 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9396 Z= 0.157 Angle : 0.650 9.604 12720 Z= 0.331 Chirality : 0.044 0.220 1405 Planarity : 0.004 0.053 1617 Dihedral : 4.437 44.993 1260 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.94 % Allowed : 25.43 % Favored : 71.63 % 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: 1.17 (0.26), residues: 1123 helix: 2.21 (0.25), residues: 444 sheet: 0.29 (0.33), residues: 250 loop : -0.41 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 164 HIS 0.003 0.001 HIS R 223 PHE 0.014 0.001 PHE R 327 TYR 0.024 0.001 TYR N 60 ARG 0.010 0.001 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 464) hydrogen bonds : angle 4.11419 ( 1344) SS BOND : bond 0.00208 ( 6) SS BOND : angle 0.97582 ( 12) covalent geometry : bond 0.00369 ( 9389) covalent geometry : angle 0.64932 (12708) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8449 (tp30) cc_final: 0.7873 (tp30) REVERT: R 37 GLN cc_start: 0.8912 (tp40) cc_final: 0.8500 (tp-100) REVERT: R 39 PHE cc_start: 0.8987 (t80) cc_final: 0.8673 (t80) REVERT: R 40 LEU cc_start: 0.9368 (mm) cc_final: 0.9138 (tp) REVERT: R 137 ASP cc_start: 0.7711 (m-30) cc_final: 0.7199 (m-30) REVERT: R 156 LEU cc_start: 0.7419 (mt) cc_final: 0.6746 (tt) REVERT: R 182 GLU cc_start: 0.7562 (tp30) cc_final: 0.7080 (tp30) REVERT: R 281 CYS cc_start: 0.6000 (OUTLIER) cc_final: 0.5713 (t) REVERT: R 407 LEU cc_start: 0.8379 (tp) cc_final: 0.8141 (tt) REVERT: R 425 MET cc_start: 0.8798 (ptm) cc_final: 0.8490 (ptm) REVERT: R 469 GLU cc_start: 0.8194 (tp30) cc_final: 0.7595 (tp30) REVERT: P 21 ARG cc_start: 0.8655 (ttm-80) cc_final: 0.8276 (tpp80) REVERT: A 27 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: A 29 GLN cc_start: 0.8424 (tp-100) cc_final: 0.8010 (tm-30) REVERT: A 34 LYS cc_start: 0.9029 (tttt) cc_final: 0.8757 (ttmm) REVERT: A 38 ARG cc_start: 0.8338 (mtm110) cc_final: 0.8137 (mtm110) REVERT: A 223 ASP cc_start: 0.8175 (t0) cc_final: 0.7930 (t0) REVERT: A 347 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8033 (ttm-80) REVERT: A 381 ASP cc_start: 0.8581 (t0) cc_final: 0.8304 (t0) REVERT: B 12 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7855 (pp20) REVERT: B 17 GLN cc_start: 0.8439 (mp10) cc_final: 0.8229 (mp10) REVERT: B 22 ARG cc_start: 0.8519 (mtt180) cc_final: 0.8174 (mtm180) REVERT: B 25 CYS cc_start: 0.8439 (m) cc_final: 0.8172 (p) REVERT: B 89 LYS cc_start: 0.8805 (mttp) cc_final: 0.8473 (mttp) REVERT: B 172 GLU cc_start: 0.8479 (tp30) cc_final: 0.8077 (tp30) REVERT: B 175 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8413 (mp10) REVERT: B 197 ARG cc_start: 0.8269 (tpp80) cc_final: 0.7407 (tpp80) REVERT: B 214 ARG cc_start: 0.7914 (ptp90) cc_final: 0.7382 (pmm-80) REVERT: B 215 GLU cc_start: 0.8274 (mp0) cc_final: 0.7472 (mp0) REVERT: B 234 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: B 254 ASP cc_start: 0.7908 (t0) cc_final: 0.7705 (OUTLIER) REVERT: B 258 ASP cc_start: 0.8243 (t0) cc_final: 0.7359 (t0) REVERT: B 303 ASP cc_start: 0.7877 (m-30) cc_final: 0.7676 (m-30) REVERT: B 325 MET cc_start: 0.8663 (mmt) cc_final: 0.8334 (mmm) REVERT: G 21 MET cc_start: 0.8689 (ttp) cc_final: 0.8469 (ppp) REVERT: G 42 GLU cc_start: 0.8494 (tt0) cc_final: 0.8293 (tt0) outliers start: 29 outliers final: 23 residues processed: 289 average time/residue: 1.5335 time to fit residues: 465.4635 Evaluate side-chains 306 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU 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 404 ARG Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 299 GLU 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 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=1.50 ------------------------------------------------------------------------------- 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: 0.1980 chunk 90 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 R 440 GLN A 357 HIS A 384 GLN B 155 ASN B 220 GLN G 18 GLN N 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.103582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088005 restraints weight = 18363.429| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.67 r_work: 0.3171 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9396 Z= 0.129 Angle : 0.656 9.729 12720 Z= 0.333 Chirality : 0.043 0.217 1405 Planarity : 0.004 0.056 1617 Dihedral : 4.312 42.828 1260 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.94 % Allowed : 26.04 % Favored : 71.02 % 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: 1.26 (0.26), residues: 1123 helix: 2.27 (0.25), residues: 443 sheet: 0.54 (0.34), residues: 239 loop : -0.46 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP R 164 HIS 0.004 0.001 HIS R 42 PHE 0.014 0.001 PHE A 212 TYR 0.025 0.001 TYR R 191 ARG 0.013 0.001 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 464) hydrogen bonds : angle 4.01631 ( 1344) SS BOND : bond 0.00207 ( 6) SS BOND : angle 0.91599 ( 12) covalent geometry : bond 0.00297 ( 9389) covalent geometry : angle 0.65578 (12708) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 289 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8434 (tp30) cc_final: 0.7847 (tp30) REVERT: R 37 GLN cc_start: 0.8880 (tp40) cc_final: 0.8477 (tp-100) REVERT: R 39 PHE cc_start: 0.8968 (t80) cc_final: 0.8719 (t80) REVERT: R 40 LEU cc_start: 0.9374 (mm) cc_final: 0.9101 (tp) REVERT: R 129 VAL cc_start: 0.8559 (t) cc_final: 0.8340 (p) REVERT: R 137 ASP cc_start: 0.7710 (m-30) cc_final: 0.7062 (m-30) REVERT: R 156 LEU cc_start: 0.7348 (mt) cc_final: 0.6685 (tt) REVERT: R 182 GLU cc_start: 0.7478 (tp30) cc_final: 0.6985 (tp30) REVERT: R 281 CYS cc_start: 0.5792 (OUTLIER) cc_final: 0.5551 (t) REVERT: R 407 LEU cc_start: 0.8362 (tp) cc_final: 0.8135 (tt) REVERT: R 425 MET cc_start: 0.8771 (ptm) cc_final: 0.8473 (ptm) REVERT: R 469 GLU cc_start: 0.8162 (tp30) cc_final: 0.7566 (tp30) REVERT: P 21 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8233 (tpp80) REVERT: A 27 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: A 29 GLN cc_start: 0.8423 (tp-100) cc_final: 0.7991 (tm-30) REVERT: A 223 ASP cc_start: 0.8175 (t0) cc_final: 0.7916 (t0) REVERT: A 347 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8089 (ttm-80) REVERT: A 381 ASP cc_start: 0.8575 (t0) cc_final: 0.8283 (t0) REVERT: B 12 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7845 (pp20) REVERT: B 13 GLN cc_start: 0.8904 (mm110) cc_final: 0.8468 (mm-40) REVERT: B 17 GLN cc_start: 0.8435 (mp10) cc_final: 0.8232 (mp10) REVERT: B 22 ARG cc_start: 0.8531 (mtt180) cc_final: 0.8148 (mtm180) REVERT: B 25 CYS cc_start: 0.8450 (m) cc_final: 0.8224 (p) REVERT: B 89 LYS cc_start: 0.8814 (mttp) cc_final: 0.8522 (mttp) REVERT: B 172 GLU cc_start: 0.8494 (tp30) cc_final: 0.8092 (tp30) REVERT: B 175 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8375 (mp10) REVERT: B 197 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7391 (tpp80) REVERT: B 214 ARG cc_start: 0.7917 (ptp90) cc_final: 0.7423 (pmm-80) REVERT: B 215 GLU cc_start: 0.8221 (mp0) cc_final: 0.7455 (mp0) REVERT: B 219 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8191 (mmt-90) REVERT: B 234 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: B 258 ASP cc_start: 0.8227 (t0) cc_final: 0.7370 (t0) REVERT: N 95 TYR cc_start: 0.9042 (m-80) cc_final: 0.8494 (m-80) outliers start: 29 outliers final: 21 residues processed: 300 average time/residue: 1.5501 time to fit residues: 488.8470 Evaluate side-chains 307 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 282 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 404 ARG Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 299 GLU 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 175 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain 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: 6.9990 chunk 88 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 100 optimal weight: 0.0010 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 110 optimal weight: 0.0670 chunk 71 optimal weight: 0.0470 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 42 HIS R 114 HIS R 440 GLN A 357 HIS B 155 ASN N 31 ASN N 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088635 restraints weight = 18469.640| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.67 r_work: 0.3185 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9396 Z= 0.129 Angle : 0.692 10.388 12720 Z= 0.348 Chirality : 0.043 0.211 1405 Planarity : 0.004 0.048 1617 Dihedral : 4.275 42.183 1260 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.63 % Allowed : 27.46 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.26), residues: 1123 helix: 2.26 (0.25), residues: 443 sheet: 0.49 (0.33), residues: 249 loop : -0.34 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 164 HIS 0.008 0.001 HIS R 42 PHE 0.016 0.001 PHE B 292 TYR 0.025 0.001 TYR R 191 ARG 0.010 0.001 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 464) hydrogen bonds : angle 4.02805 ( 1344) SS BOND : bond 0.00166 ( 6) SS BOND : angle 1.08603 ( 12) covalent geometry : bond 0.00299 ( 9389) covalent geometry : angle 0.69173 (12708) Misc. bond : bond 0.00000 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 287 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8433 (tp30) cc_final: 0.7841 (tp30) REVERT: R 37 GLN cc_start: 0.8875 (tp40) cc_final: 0.8467 (tp-100) REVERT: R 39 PHE cc_start: 0.8960 (t80) cc_final: 0.8729 (t80) REVERT: R 40 LEU cc_start: 0.9384 (mm) cc_final: 0.9100 (tp) REVERT: R 129 VAL cc_start: 0.8590 (t) cc_final: 0.8376 (p) REVERT: R 137 ASP cc_start: 0.7698 (m-30) cc_final: 0.7014 (m-30) REVERT: R 156 LEU cc_start: 0.7294 (mt) cc_final: 0.6638 (tt) REVERT: R 182 GLU cc_start: 0.7399 (tp30) cc_final: 0.6913 (tp30) REVERT: R 217 CYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6900 (p) REVERT: R 407 LEU cc_start: 0.8368 (tp) cc_final: 0.8140 (tt) REVERT: R 425 MET cc_start: 0.8773 (ptm) cc_final: 0.8493 (ptm) REVERT: R 469 GLU cc_start: 0.8151 (tp30) cc_final: 0.7542 (tp30) REVERT: P 21 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8255 (tpp80) REVERT: A 27 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: A 29 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8030 (tm-30) REVERT: A 223 ASP cc_start: 0.8171 (t0) cc_final: 0.7928 (t0) REVERT: A 347 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.8072 (ttm-80) REVERT: A 381 ASP cc_start: 0.8589 (t0) cc_final: 0.8290 (t0) REVERT: B 12 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7678 (pp20) REVERT: B 17 GLN cc_start: 0.8460 (mp10) cc_final: 0.8229 (mp10) REVERT: B 22 ARG cc_start: 0.8490 (mtt180) cc_final: 0.8056 (mtm180) REVERT: B 25 CYS cc_start: 0.8441 (m) cc_final: 0.8222 (p) REVERT: B 76 ASP cc_start: 0.8501 (p0) cc_final: 0.7977 (p0) REVERT: B 89 LYS cc_start: 0.8809 (mttp) cc_final: 0.8515 (mttp) REVERT: B 172 GLU cc_start: 0.8490 (tp30) cc_final: 0.8099 (tp30) REVERT: B 175 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8379 (mp10) REVERT: B 197 ARG cc_start: 0.8238 (tpp80) cc_final: 0.7382 (tpp80) REVERT: B 214 ARG cc_start: 0.7900 (ptp90) cc_final: 0.7502 (pmm-80) REVERT: B 215 GLU cc_start: 0.8185 (mp0) cc_final: 0.7392 (mp0) REVERT: B 219 ARG cc_start: 0.8415 (tpp80) cc_final: 0.8185 (mmm-85) REVERT: B 234 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: B 258 ASP cc_start: 0.8213 (t0) cc_final: 0.7199 (t0) REVERT: N 13 GLN cc_start: 0.8275 (pp30) cc_final: 0.8061 (mm-40) REVERT: N 95 TYR cc_start: 0.9008 (m-80) cc_final: 0.8403 (m-80) outliers start: 26 outliers final: 19 residues processed: 295 average time/residue: 1.5192 time to fit residues: 471.3109 Evaluate side-chains 301 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 278 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 444 GLU 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 299 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain 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: 5.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS R 374 ASN R 440 GLN A 357 HIS B 268 ASN N 31 ASN N 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086655 restraints weight = 18504.731| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.66 r_work: 0.3145 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9396 Z= 0.172 Angle : 0.713 11.039 12720 Z= 0.363 Chirality : 0.045 0.205 1405 Planarity : 0.005 0.061 1617 Dihedral : 4.430 44.379 1260 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.63 % Allowed : 27.56 % Favored : 69.81 % 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: 1.16 (0.26), residues: 1123 helix: 2.17 (0.25), residues: 443 sheet: 0.39 (0.33), residues: 249 loop : -0.43 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 164 HIS 0.014 0.001 HIS R 42 PHE 0.024 0.001 PHE R 327 TYR 0.023 0.001 TYR R 191 ARG 0.013 0.001 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 464) hydrogen bonds : angle 4.11686 ( 1344) SS BOND : bond 0.00241 ( 6) SS BOND : angle 1.28914 ( 12) covalent geometry : bond 0.00409 ( 9389) covalent geometry : angle 0.71183 (12708) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8744.58 seconds wall clock time: 150 minutes 58.07 seconds (9058.07 seconds total)