Starting phenix.real_space_refine on Sat Dec 28 21:55:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y35_33588/12_2024/7y35_33588.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y35_33588/12_2024/7y35_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_33588/12_2024/7y35_33588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y35_33588/12_2024/7y35_33588.map" model { file = "/net/cci-nas-00/data/ceres_data/7y35_33588/12_2024/7y35_33588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y35_33588/12_2024/7y35_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-5532/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: 5.67, per 1000 atoms: 0.62 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: 2.60 Conformation dependent library (CDL) restraints added in 1.0 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: 1.02 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: 2.76 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1492 1.31 - 1.44: 2658 1.44 - 1.57: 5161 1.57 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 9389 Sorted by residual: bond pdb=" CA PHE R 173 " pdb=" C PHE R 173 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.32e-02 5.74e+03 2.10e+01 bond pdb=" C GLU R 180 " pdb=" O GLU R 180 " ideal model delta sigma weight residual 1.236 1.182 0.055 1.47e-02 4.63e+03 1.38e+01 bond pdb=" N GLU R 177 " pdb=" CA GLU R 177 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.30e+01 bond pdb=" CA GLU R 177 " pdb=" C GLU R 177 " ideal model delta sigma weight residual 1.523 1.566 -0.043 1.34e-02 5.57e+03 1.03e+01 bond pdb=" N THR R 175 " pdb=" CA THR R 175 " ideal model delta sigma weight residual 1.457 1.423 0.035 1.29e-02 6.01e+03 7.27e+00 ... (remaining 9384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 12632 3.45 - 6.90: 68 6.90 - 10.35: 5 10.35 - 13.79: 1 13.79 - 17.24: 2 Bond angle restraints: 12708 Sorted by residual: angle pdb=" CA LYS R 172 " pdb=" C LYS R 172 " pdb=" N PHE R 173 " ideal model delta sigma weight residual 117.63 100.39 17.24 1.25e+00 6.40e-01 1.90e+02 angle pdb=" C LYS R 172 " pdb=" N PHE R 173 " pdb=" CA PHE R 173 " ideal model delta sigma weight residual 120.54 136.29 -15.75 1.35e+00 5.49e-01 1.36e+02 angle pdb=" O LYS R 172 " pdb=" C LYS R 172 " pdb=" N PHE R 173 " ideal model delta sigma weight residual 122.22 133.17 -10.95 1.17e+00 7.31e-01 8.75e+01 angle pdb=" N ASN R 176 " pdb=" CA ASN R 176 " pdb=" C ASN R 176 " ideal model delta sigma weight residual 112.23 120.32 -8.09 1.26e+00 6.30e-01 4.12e+01 angle pdb=" C ASN R 176 " pdb=" N GLU R 177 " pdb=" CA GLU R 177 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 ... (remaining 12703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 5084 16.82 - 33.64: 391 33.64 - 50.46: 77 50.46 - 67.28: 11 67.28 - 84.11: 11 Dihedral angle restraints: 5574 sinusoidal: 2231 harmonic: 3343 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -9.29 -76.71 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 5571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 846 0.040 - 0.081: 380 0.081 - 0.121: 145 0.121 - 0.162: 30 0.162 - 0.202: 4 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA PHE R 335 " pdb=" N PHE R 335 " pdb=" C PHE R 335 " pdb=" CB PHE R 335 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA TYR R 191 " pdb=" N TYR R 191 " pdb=" C TYR R 191 " pdb=" CB TYR R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA VAL R 157 " pdb=" N VAL R 157 " pdb=" C VAL R 157 " pdb=" CB VAL R 157 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 1402 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS R 172 " 0.032 2.00e-02 2.50e+03 7.65e-02 5.85e+01 pdb=" C LYS R 172 " -0.132 2.00e-02 2.50e+03 pdb=" O LYS R 172 " 0.056 2.00e-02 2.50e+03 pdb=" N PHE R 173 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO B 236 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 175 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C THR R 175 " -0.042 2.00e-02 2.50e+03 pdb=" O THR R 175 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN R 176 " 0.014 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1441 2.75 - 3.29: 8451 3.29 - 3.83: 15173 3.83 - 4.36: 18199 4.36 - 4.90: 31860 Nonbonded interactions: 75124 Sorted by model distance: nonbonded pdb=" ND2 ASN R 448 " pdb=" OE2 GLU P 4 " model vdw 2.217 3.120 nonbonded pdb=" NH1 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.226 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.264 3.040 nonbonded pdb=" OE2 GLU A 27 " pdb=" NZ LYS B 89 " model vdw 2.306 3.120 nonbonded pdb=" NE1 TRP R 437 " pdb=" OD2 ASP P 10 " model vdw 2.341 3.120 ... (remaining 75119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.670 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 9389 Z= 0.586 Angle : 0.795 17.243 12708 Z= 0.477 Chirality : 0.052 0.202 1405 Planarity : 0.005 0.076 1617 Dihedral : 12.994 84.106 3394 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1123 helix: -0.13 (0.23), residues: 440 sheet: -1.02 (0.30), residues: 258 loop : -1.51 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 99 HIS 0.016 0.002 HIS A 357 PHE 0.022 0.002 PHE R 335 TYR 0.042 0.002 TYR B 59 ARG 0.005 0.001 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 0.930 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: 1.5749 time to fit residues: 571.9832 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 : 1.081 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9389 Z= 0.201 Angle : 0.608 7.618 12708 Z= 0.323 Chirality : 0.043 0.236 1405 Planarity : 0.005 0.059 1617 Dihedral : 4.940 52.044 1260 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.44 % Allowed : 16.21 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1123 helix: 1.07 (0.25), residues: 456 sheet: -0.17 (0.33), residues: 229 loop : -1.36 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 352 HIS 0.004 0.001 HIS R 114 PHE 0.020 0.001 PHE R 314 TYR 0.026 0.001 TYR R 191 ARG 0.008 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8855 (mp0) cc_final: 0.8536 (mp0) REVERT: R 37 GLN cc_start: 0.9003 (tp40) cc_final: 0.8544 (tp40) REVERT: R 39 PHE cc_start: 0.8957 (t80) cc_final: 0.8623 (t80) REVERT: R 43 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8277 (mmm160) REVERT: R 47 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8710 (mm110) REVERT: R 149 ASP cc_start: 0.7863 (t70) cc_final: 0.7597 (t0) REVERT: R 150 ARG cc_start: 0.6555 (mmm160) cc_final: 0.6331 (ttp80) REVERT: R 156 LEU cc_start: 0.7180 (mt) cc_final: 0.6680 (tt) REVERT: R 160 HIS cc_start: 0.7359 (m90) cc_final: 0.6671 (m90) REVERT: R 182 GLU cc_start: 0.7053 (tp30) cc_final: 0.6703 (tp30) REVERT: R 207 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8406 (mm) REVERT: R 346 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8521 (mt) REVERT: R 407 LEU cc_start: 0.8428 (tp) cc_final: 0.8140 (tt) REVERT: A 17 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7860 (mmtm) REVERT: A 27 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: A 34 LYS cc_start: 0.8931 (tttt) cc_final: 0.8593 (ttmm) REVERT: A 38 ARG cc_start: 0.7675 (mtm110) cc_final: 0.7472 (mtm110) REVERT: A 46 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8033 (tt) REVERT: A 54 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8795 (t) REVERT: A 311 TYR cc_start: 0.8158 (m-80) cc_final: 0.7834 (m-80) REVERT: A 343 ASP cc_start: 0.8403 (m-30) cc_final: 0.8088 (m-30) REVERT: B 12 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7806 (pp20) REVERT: B 22 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7210 (mtm-85) REVERT: B 25 CYS cc_start: 0.8167 (m) cc_final: 0.7727 (p) REVERT: B 32 GLN cc_start: 0.8091 (mt0) cc_final: 0.7715 (mt0) REVERT: B 46 ARG cc_start: 0.7424 (mtp180) cc_final: 0.7185 (ttm110) REVERT: B 75 GLN cc_start: 0.8418 (mt0) cc_final: 0.8109 (mt0) REVERT: B 89 LYS cc_start: 0.8667 (mttp) cc_final: 0.8176 (mttp) REVERT: B 214 ARG cc_start: 0.7771 (ptp90) cc_final: 0.7331 (ptp90) REVERT: B 215 GLU cc_start: 0.7728 (mp0) cc_final: 0.7514 (mp0) REVERT: B 258 ASP cc_start: 0.8010 (t0) cc_final: 0.6586 (t0) REVERT: N 25 SER cc_start: 0.7911 (t) cc_final: 0.7689 (m) REVERT: N 43 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8290 (mmtt) REVERT: N 69 THR cc_start: 0.8682 (m) cc_final: 0.8193 (p) REVERT: N 78 THR cc_start: 0.8783 (t) cc_final: 0.8525 (p) REVERT: N 83 MET cc_start: 0.8262 (mtp) cc_final: 0.8057 (mtm) REVERT: N 123 GLN cc_start: 0.8660 (tp40) cc_final: 0.8440 (tm-30) outliers start: 34 outliers final: 17 residues processed: 311 average time/residue: 1.5001 time to fit residues: 491.5182 Evaluate side-chains 307 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 285 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.0000 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9389 Z= 0.217 Angle : 0.590 8.680 12708 Z= 0.310 Chirality : 0.043 0.235 1405 Planarity : 0.004 0.055 1617 Dihedral : 4.625 46.550 1260 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.26 % Allowed : 19.15 % Favored : 76.60 % 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: 0.48 (0.26), residues: 1123 helix: 1.72 (0.25), residues: 448 sheet: -0.02 (0.34), residues: 241 loop : -0.93 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 164 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE R 314 TYR 0.025 0.001 TYR R 191 ARG 0.007 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 283 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8857 (mp0) cc_final: 0.8511 (mp0) REVERT: R 36 GLU cc_start: 0.8475 (tp30) cc_final: 0.7712 (tp30) REVERT: R 37 GLN cc_start: 0.9049 (tp40) cc_final: 0.8547 (tp40) REVERT: R 39 PHE cc_start: 0.8969 (t80) cc_final: 0.8575 (t80) REVERT: R 40 LEU cc_start: 0.9310 (mm) cc_final: 0.8791 (mm) REVERT: R 43 ARG cc_start: 0.8813 (mmm160) cc_final: 0.8358 (mmm160) REVERT: R 47 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8771 (mm110) REVERT: R 137 ASP cc_start: 0.7968 (m-30) cc_final: 0.7749 (m-30) REVERT: R 156 LEU cc_start: 0.7154 (mt) cc_final: 0.6498 (tt) REVERT: R 160 HIS cc_start: 0.7623 (m90) cc_final: 0.6996 (m90) REVERT: R 182 GLU cc_start: 0.7068 (tp30) cc_final: 0.6687 (tp30) REVERT: R 207 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8423 (mm) REVERT: R 346 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8564 (mt) REVERT: R 407 LEU cc_start: 0.8429 (tp) cc_final: 0.8181 (tt) REVERT: R 425 MET cc_start: 0.7477 (ptm) cc_final: 0.7272 (ptm) REVERT: P 26 LYS cc_start: 0.8986 (tmmt) cc_final: 0.8687 (tmmt) REVERT: P 27 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8303 (mm) REVERT: A 17 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7998 (mmtm) REVERT: A 27 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: A 34 LYS cc_start: 0.8932 (tttt) cc_final: 0.8724 (ttmm) REVERT: A 46 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8015 (tt) REVERT: A 311 TYR cc_start: 0.8178 (m-80) cc_final: 0.7838 (m-80) REVERT: B 22 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7314 (mtm-85) REVERT: B 25 CYS cc_start: 0.8136 (m) cc_final: 0.7786 (p) REVERT: B 32 GLN cc_start: 0.8074 (mt0) cc_final: 0.7711 (mt0) REVERT: B 89 LYS cc_start: 0.8644 (mttp) cc_final: 0.8276 (mttp) REVERT: B 214 ARG cc_start: 0.7719 (ptp90) cc_final: 0.7228 (ptp90) REVERT: B 234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: B 258 ASP cc_start: 0.7959 (t0) cc_final: 0.6524 (t0) REVERT: N 25 SER cc_start: 0.7993 (t) cc_final: 0.7607 (p) REVERT: N 35 ASN cc_start: 0.8737 (m-40) cc_final: 0.8354 (m-40) REVERT: N 69 THR cc_start: 0.8759 (m) cc_final: 0.8292 (p) REVERT: N 78 THR cc_start: 0.8837 (t) cc_final: 0.8539 (p) REVERT: N 123 GLN cc_start: 0.8767 (tp40) cc_final: 0.8507 (tm-30) outliers start: 42 outliers final: 22 residues processed: 301 average time/residue: 1.5730 time to fit residues: 499.9522 Evaluate side-chains 303 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 1.857 ------------------------------------------------------------------------------- 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 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 27 LEU 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 327 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 0.0020 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 440 GLN A 357 HIS B 75 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9389 Z= 0.196 Angle : 0.583 8.779 12708 Z= 0.305 Chirality : 0.042 0.186 1405 Planarity : 0.004 0.051 1617 Dihedral : 4.473 44.841 1260 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.85 % Allowed : 20.16 % Favored : 75.99 % 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: 0.84 (0.26), residues: 1123 helix: 1.97 (0.26), residues: 450 sheet: 0.34 (0.34), residues: 237 loop : -0.80 (0.29), residues: 436 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 R 335 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.001 ARG A 333 *********************** 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 324 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8863 (mp0) cc_final: 0.8474 (mp0) REVERT: R 36 GLU cc_start: 0.8428 (tp30) cc_final: 0.7587 (tp30) REVERT: R 37 GLN cc_start: 0.9106 (tp40) cc_final: 0.8609 (tp40) REVERT: R 39 PHE cc_start: 0.8942 (t80) cc_final: 0.8524 (t80) REVERT: R 40 LEU cc_start: 0.9310 (mm) cc_final: 0.8526 (mt) REVERT: R 43 ARG cc_start: 0.8808 (mmm160) cc_final: 0.8397 (mmm160) REVERT: R 47 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8771 (mm-40) REVERT: R 156 LEU cc_start: 0.7074 (mt) cc_final: 0.6398 (tt) REVERT: R 160 HIS cc_start: 0.7630 (m90) cc_final: 0.7007 (m90) REVERT: R 182 GLU cc_start: 0.7137 (tp30) cc_final: 0.6738 (tp30) REVERT: R 207 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8386 (mm) REVERT: R 407 LEU cc_start: 0.8440 (tp) cc_final: 0.8221 (tt) REVERT: P 21 ARG cc_start: 0.8712 (ttm-80) cc_final: 0.8397 (tpp80) REVERT: P 26 LYS cc_start: 0.9000 (tmmt) cc_final: 0.8652 (tmmt) REVERT: P 27 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8011 (mm) REVERT: A 17 LYS cc_start: 0.8281 (mmtm) cc_final: 0.8045 (mmtm) REVERT: A 27 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: A 46 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7972 (tt) REVERT: A 311 TYR cc_start: 0.8198 (m-80) cc_final: 0.7946 (m-80) REVERT: B 5 ASP cc_start: 0.7961 (p0) cc_final: 0.7603 (p0) REVERT: B 12 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7780 (pp20) REVERT: B 22 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7519 (mtm180) REVERT: B 25 CYS cc_start: 0.8077 (m) cc_final: 0.7828 (p) REVERT: B 32 GLN cc_start: 0.7999 (mt0) cc_final: 0.7599 (mt0) REVERT: B 59 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: B 75 GLN cc_start: 0.8299 (mt0) cc_final: 0.8098 (mt0) REVERT: B 89 LYS cc_start: 0.8654 (mttp) cc_final: 0.8270 (mttp) REVERT: B 215 GLU cc_start: 0.7815 (mp0) cc_final: 0.7288 (mp0) REVERT: B 234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: B 254 ASP cc_start: 0.7485 (t0) cc_final: 0.7262 (t0) REVERT: B 258 ASP cc_start: 0.7960 (t0) cc_final: 0.7004 (t0) REVERT: G 18 GLN cc_start: 0.8607 (tp40) cc_final: 0.7952 (tp40) REVERT: G 20 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8644 (mtpt) REVERT: N 25 SER cc_start: 0.8105 (t) cc_final: 0.7751 (p) REVERT: N 35 ASN cc_start: 0.8738 (m-40) cc_final: 0.8427 (m-40) REVERT: N 69 THR cc_start: 0.8760 (m) cc_final: 0.8321 (p) REVERT: N 78 THR cc_start: 0.8903 (t) cc_final: 0.8551 (p) REVERT: N 114 THR cc_start: 0.8870 (t) cc_final: 0.8509 (p) REVERT: N 123 GLN cc_start: 0.8747 (tp40) cc_final: 0.8480 (tm-30) outliers start: 38 outliers final: 20 residues processed: 300 average time/residue: 1.5160 time to fit residues: 479.0664 Evaluate side-chains 303 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 27 LEU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 0.0470 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 1.2682 ------------------------------------------------------------------------------- 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 278 ASN A 357 HIS N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9389 Z= 0.268 Angle : 0.604 8.637 12708 Z= 0.318 Chirality : 0.043 0.182 1405 Planarity : 0.004 0.055 1617 Dihedral : 4.525 46.410 1260 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.05 % Allowed : 21.18 % Favored : 74.77 % 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: 0.98 (0.26), residues: 1123 helix: 2.09 (0.26), residues: 445 sheet: 0.38 (0.34), residues: 239 loop : -0.69 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 164 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE B 151 TYR 0.023 0.001 TYR R 191 ARG 0.009 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8859 (mp0) cc_final: 0.8435 (mp0) REVERT: R 36 GLU cc_start: 0.8417 (tp30) cc_final: 0.7872 (tp30) REVERT: R 37 GLN cc_start: 0.9146 (tp40) cc_final: 0.8596 (tp-100) REVERT: R 39 PHE cc_start: 0.8958 (t80) cc_final: 0.8583 (t80) REVERT: R 40 LEU cc_start: 0.9324 (mm) cc_final: 0.9061 (tp) REVERT: R 43 ARG cc_start: 0.8818 (mmm160) cc_final: 0.8405 (mmm160) REVERT: R 47 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8734 (mm-40) REVERT: R 137 ASP cc_start: 0.8368 (m-30) cc_final: 0.7795 (m-30) REVERT: R 154 TRP cc_start: 0.6766 (m100) cc_final: 0.6539 (m100) REVERT: R 156 LEU cc_start: 0.7195 (mt) cc_final: 0.6438 (tt) REVERT: R 182 GLU cc_start: 0.7241 (tp30) cc_final: 0.6857 (tp30) REVERT: R 207 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8426 (mm) REVERT: R 281 CYS cc_start: 0.5154 (t) cc_final: 0.4882 (t) REVERT: R 405 LYS cc_start: 0.8384 (tppp) cc_final: 0.8140 (tppp) REVERT: R 407 LEU cc_start: 0.8447 (tp) cc_final: 0.8240 (tt) REVERT: P 21 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8281 (tpp80) REVERT: P 26 LYS cc_start: 0.9047 (tmmt) cc_final: 0.8672 (tmmt) REVERT: A 17 LYS cc_start: 0.8320 (mmtm) cc_final: 0.8087 (mmtm) REVERT: A 27 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: A 29 GLN cc_start: 0.8245 (tp-100) cc_final: 0.7826 (tm-30) REVERT: A 46 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 381 ASP cc_start: 0.8255 (t0) cc_final: 0.8053 (t0) REVERT: B 12 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7810 (pp20) REVERT: B 22 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7581 (mtm180) REVERT: B 25 CYS cc_start: 0.8170 (m) cc_final: 0.7857 (p) REVERT: B 32 GLN cc_start: 0.8037 (mt0) cc_final: 0.7639 (mt0) REVERT: B 59 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8423 (m-80) REVERT: B 89 LYS cc_start: 0.8641 (mttp) cc_final: 0.8269 (mttp) REVERT: B 197 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7216 (tpp80) REVERT: B 214 ARG cc_start: 0.7581 (ptp90) cc_final: 0.6966 (ptp90) REVERT: B 215 GLU cc_start: 0.7837 (mp0) cc_final: 0.7382 (mp0) REVERT: B 234 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: B 254 ASP cc_start: 0.7564 (t0) cc_final: 0.7251 (t0) REVERT: B 258 ASP cc_start: 0.7987 (t0) cc_final: 0.6972 (t0) REVERT: G 18 GLN cc_start: 0.8645 (tp40) cc_final: 0.8072 (tp40) REVERT: G 20 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8706 (mtpt) REVERT: N 90 ASP cc_start: 0.8880 (m-30) cc_final: 0.8656 (m-30) REVERT: N 123 GLN cc_start: 0.8777 (tp40) cc_final: 0.8552 (tm-30) outliers start: 40 outliers final: 21 residues processed: 294 average time/residue: 1.5492 time to fit residues: 480.3453 Evaluate side-chains 303 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 275 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 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS A 357 HIS N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9389 Z= 0.218 Angle : 0.596 9.335 12708 Z= 0.311 Chirality : 0.042 0.185 1405 Planarity : 0.004 0.052 1617 Dihedral : 4.437 44.667 1260 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.56 % Allowed : 21.68 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1123 helix: 2.21 (0.26), residues: 444 sheet: 0.44 (0.34), residues: 239 loop : -0.61 (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 B 241 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.001 ARG R 51 *********************** 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 327 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 282 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8837 (mp0) cc_final: 0.8420 (mp0) REVERT: R 36 GLU cc_start: 0.8486 (tp30) cc_final: 0.7846 (tp30) REVERT: R 37 GLN cc_start: 0.9161 (tp40) cc_final: 0.8576 (tp-100) REVERT: R 39 PHE cc_start: 0.8943 (t80) cc_final: 0.8598 (t80) REVERT: R 40 LEU cc_start: 0.9321 (mm) cc_final: 0.9032 (tp) REVERT: R 43 ARG cc_start: 0.8793 (mmm160) cc_final: 0.8363 (mmm160) REVERT: R 47 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8906 (mm-40) REVERT: R 137 ASP cc_start: 0.8399 (m-30) cc_final: 0.7717 (m-30) REVERT: R 154 TRP cc_start: 0.6692 (m100) cc_final: 0.6474 (m100) REVERT: R 156 LEU cc_start: 0.7227 (mt) cc_final: 0.6484 (tt) REVERT: R 182 GLU cc_start: 0.7068 (tp30) cc_final: 0.6598 (tp30) REVERT: R 281 CYS cc_start: 0.4951 (OUTLIER) cc_final: 0.4647 (t) REVERT: R 407 LEU cc_start: 0.8446 (tp) cc_final: 0.8241 (tt) REVERT: R 469 GLU cc_start: 0.7594 (tp30) cc_final: 0.7117 (tp30) REVERT: P 21 ARG cc_start: 0.8671 (ttm-80) cc_final: 0.8220 (tpp80) REVERT: P 26 LYS cc_start: 0.9022 (tmmt) cc_final: 0.8648 (tmmt) REVERT: P 27 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7628 (mm) REVERT: A 27 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6645 (mp0) REVERT: A 29 GLN cc_start: 0.8282 (tp-100) cc_final: 0.7712 (tm-30) REVERT: A 55 THR cc_start: 0.8661 (m) cc_final: 0.8453 (p) REVERT: A 271 LYS cc_start: 0.8223 (mmtp) cc_final: 0.8016 (mttp) REVERT: A 311 TYR cc_start: 0.8286 (m-80) cc_final: 0.7998 (m-10) REVERT: A 336 ARG cc_start: 0.7846 (ttt-90) cc_final: 0.7597 (ttt-90) REVERT: A 381 ASP cc_start: 0.8248 (t0) cc_final: 0.8034 (t0) REVERT: B 12 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7748 (pp20) REVERT: B 22 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7738 (mtm180) REVERT: B 25 CYS cc_start: 0.8206 (m) cc_final: 0.7912 (p) REVERT: B 32 GLN cc_start: 0.7993 (mt0) cc_final: 0.7590 (mt0) REVERT: B 59 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: B 75 GLN cc_start: 0.8316 (mt0) cc_final: 0.7629 (mt0) REVERT: B 89 LYS cc_start: 0.8650 (mttp) cc_final: 0.8288 (mttp) REVERT: B 175 GLN cc_start: 0.8534 (tp40) cc_final: 0.7943 (mp10) REVERT: B 197 ARG cc_start: 0.7786 (tpp80) cc_final: 0.6938 (tpp80) REVERT: B 214 ARG cc_start: 0.7588 (ptp90) cc_final: 0.7020 (pmm-80) REVERT: B 215 GLU cc_start: 0.7889 (mp0) cc_final: 0.7035 (mp0) REVERT: B 219 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7817 (mmt-90) REVERT: B 234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: B 254 ASP cc_start: 0.7513 (t0) cc_final: 0.7274 (OUTLIER) REVERT: B 258 ASP cc_start: 0.7994 (t0) cc_final: 0.6961 (t0) REVERT: G 18 GLN cc_start: 0.8697 (tp40) cc_final: 0.8115 (tp40) REVERT: N 13 GLN cc_start: 0.8268 (pp30) cc_final: 0.8048 (mm-40) REVERT: N 35 ASN cc_start: 0.8741 (m-40) cc_final: 0.8416 (m-40) REVERT: N 90 ASP cc_start: 0.8829 (m-30) cc_final: 0.8619 (m-30) REVERT: N 123 GLN cc_start: 0.8744 (tp40) cc_final: 0.8501 (tm-30) outliers start: 45 outliers final: 22 residues processed: 300 average time/residue: 1.5981 time to fit residues: 504.2540 Evaluate side-chains 297 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 27 LEU 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 207 ILE 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 B residue 59 TYR 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 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 236 GLN A 357 HIS A 384 GLN N 31 ASN N 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9389 Z= 0.200 Angle : 0.621 10.251 12708 Z= 0.318 Chirality : 0.042 0.204 1405 Planarity : 0.004 0.052 1617 Dihedral : 4.369 44.252 1260 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.55 % Allowed : 24.32 % 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: 1.19 (0.26), residues: 1123 helix: 2.27 (0.25), residues: 444 sheet: 0.48 (0.33), residues: 239 loop : -0.57 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 164 HIS 0.002 0.001 HIS P 32 PHE 0.011 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.001 ARG R 390 *********************** 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 316 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8865 (mp0) cc_final: 0.8428 (mp0) REVERT: R 36 GLU cc_start: 0.8478 (tp30) cc_final: 0.7758 (tp30) REVERT: R 37 GLN cc_start: 0.9168 (tp40) cc_final: 0.8591 (tp-100) REVERT: R 39 PHE cc_start: 0.8922 (t80) cc_final: 0.8604 (t80) REVERT: R 40 LEU cc_start: 0.9320 (mm) cc_final: 0.9058 (tp) REVERT: R 43 ARG cc_start: 0.8817 (mmm160) cc_final: 0.8332 (mmm160) REVERT: R 47 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8946 (mm110) REVERT: R 137 ASP cc_start: 0.8390 (m-30) cc_final: 0.7743 (m-30) REVERT: R 154 TRP cc_start: 0.6690 (m100) cc_final: 0.6418 (m100) REVERT: R 156 LEU cc_start: 0.7136 (mt) cc_final: 0.6426 (tt) REVERT: R 169 GLU cc_start: 0.9129 (tt0) cc_final: 0.8887 (tt0) REVERT: R 182 GLU cc_start: 0.7087 (tp30) cc_final: 0.6610 (tp30) REVERT: R 281 CYS cc_start: 0.4912 (OUTLIER) cc_final: 0.4637 (t) REVERT: R 469 GLU cc_start: 0.7604 (tp30) cc_final: 0.7059 (tp30) REVERT: P 21 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8375 (ttm-80) REVERT: A 27 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: A 29 GLN cc_start: 0.8342 (tp-100) cc_final: 0.7782 (tm-30) REVERT: A 271 LYS cc_start: 0.8246 (mmtp) cc_final: 0.8000 (mttp) REVERT: A 311 TYR cc_start: 0.8255 (m-80) cc_final: 0.7989 (m-10) REVERT: A 336 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7596 (ttt-90) REVERT: A 381 ASP cc_start: 0.8253 (t0) cc_final: 0.8037 (t0) REVERT: B 13 GLN cc_start: 0.8636 (mm110) cc_final: 0.8338 (mm-40) REVERT: B 22 ARG cc_start: 0.8230 (mtt180) cc_final: 0.7787 (mtm180) REVERT: B 25 CYS cc_start: 0.8141 (m) cc_final: 0.7909 (p) REVERT: B 59 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: B 75 GLN cc_start: 0.8182 (mt0) cc_final: 0.7857 (mt0) REVERT: B 89 LYS cc_start: 0.8661 (mttp) cc_final: 0.8290 (mttp) REVERT: B 172 GLU cc_start: 0.7973 (tp30) cc_final: 0.7622 (tp30) REVERT: B 175 GLN cc_start: 0.8533 (tp40) cc_final: 0.7939 (mp10) REVERT: B 197 ARG cc_start: 0.7801 (tpp80) cc_final: 0.6901 (tpp80) REVERT: B 214 ARG cc_start: 0.7577 (ptp90) cc_final: 0.7196 (pmm-80) REVERT: B 219 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7870 (mmt-90) REVERT: B 234 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: B 254 ASP cc_start: 0.7488 (t0) cc_final: 0.7275 (OUTLIER) REVERT: B 258 ASP cc_start: 0.8003 (t0) cc_final: 0.6961 (t0) REVERT: G 18 GLN cc_start: 0.8679 (tp40) cc_final: 0.8402 (tp-100) REVERT: N 35 ASN cc_start: 0.8729 (m-40) cc_final: 0.8451 (m-40) REVERT: N 123 GLN cc_start: 0.8748 (tp40) cc_final: 0.8441 (tm-30) outliers start: 35 outliers final: 23 residues processed: 295 average time/residue: 1.6074 time to fit residues: 498.0280 Evaluate side-chains 303 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 114 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 322 TRP 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 33 ASP Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR 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 N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS R 440 GLN A 357 HIS N 31 ASN N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9389 Z= 0.216 Angle : 0.650 12.443 12708 Z= 0.328 Chirality : 0.043 0.219 1405 Planarity : 0.004 0.054 1617 Dihedral : 4.348 44.224 1260 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.14 % Allowed : 25.84 % 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: 1.18 (0.26), residues: 1123 helix: 2.26 (0.25), residues: 443 sheet: 0.52 (0.33), residues: 240 loop : -0.59 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 164 HIS 0.003 0.001 HIS R 140 PHE 0.013 0.001 PHE B 292 TYR 0.024 0.001 TYR R 191 ARG 0.010 0.001 ARG R 51 *********************** 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 310 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 1.019 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 35 GLU cc_start: 0.8848 (mp0) cc_final: 0.8439 (mp0) REVERT: R 36 GLU cc_start: 0.8458 (tp30) cc_final: 0.7736 (tp30) REVERT: R 37 GLN cc_start: 0.9170 (tp40) cc_final: 0.8602 (tp-100) REVERT: R 39 PHE cc_start: 0.8897 (t80) cc_final: 0.8575 (t80) REVERT: R 40 LEU cc_start: 0.9322 (mm) cc_final: 0.9038 (tp) REVERT: R 43 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8346 (mmm160) REVERT: R 47 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8829 (mm-40) REVERT: R 137 ASP cc_start: 0.8404 (m-30) cc_final: 0.7846 (m-30) REVERT: R 154 TRP cc_start: 0.6661 (m100) cc_final: 0.6394 (m100) REVERT: R 156 LEU cc_start: 0.7075 (mt) cc_final: 0.6364 (tt) REVERT: R 182 GLU cc_start: 0.7099 (tp30) cc_final: 0.6607 (tp30) REVERT: R 281 CYS cc_start: 0.4907 (OUTLIER) cc_final: 0.4630 (t) REVERT: R 469 GLU cc_start: 0.7613 (tp30) cc_final: 0.7076 (tp30) REVERT: P 26 LYS cc_start: 0.9003 (tmmt) cc_final: 0.8624 (tmmt) REVERT: A 27 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: A 29 GLN cc_start: 0.8310 (tp-100) cc_final: 0.7787 (tm-30) REVERT: A 311 TYR cc_start: 0.8224 (m-80) cc_final: 0.7930 (m-10) REVERT: A 336 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7601 (ttt-90) REVERT: A 381 ASP cc_start: 0.8271 (t0) cc_final: 0.8054 (t0) REVERT: B 22 ARG cc_start: 0.8264 (mtt180) cc_final: 0.7813 (mtm180) REVERT: B 25 CYS cc_start: 0.8122 (m) cc_final: 0.7922 (p) REVERT: B 59 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8409 (m-80) REVERT: B 89 LYS cc_start: 0.8661 (mttp) cc_final: 0.8278 (mttp) REVERT: B 172 GLU cc_start: 0.7997 (tp30) cc_final: 0.7645 (tp30) REVERT: B 197 ARG cc_start: 0.7797 (tpp80) cc_final: 0.6864 (tpp80) REVERT: B 214 ARG cc_start: 0.7568 (ptp90) cc_final: 0.7217 (pmm-80) REVERT: B 219 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7845 (mmt-90) REVERT: B 234 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: B 258 ASP cc_start: 0.8003 (t0) cc_final: 0.6965 (t0) REVERT: G 18 GLN cc_start: 0.8643 (tp40) cc_final: 0.8375 (tp-100) REVERT: N 35 ASN cc_start: 0.8733 (m-40) cc_final: 0.8458 (m-40) REVERT: N 123 GLN cc_start: 0.8749 (tp40) cc_final: 0.8442 (tm-30) outliers start: 31 outliers final: 22 residues processed: 292 average time/residue: 1.6037 time to fit residues: 491.5816 Evaluate side-chains 302 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 114 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 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 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 B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 R 374 ASN R 440 GLN A 357 HIS A 384 GLN N 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9389 Z= 0.203 Angle : 0.656 11.046 12708 Z= 0.333 Chirality : 0.043 0.217 1405 Planarity : 0.004 0.053 1617 Dihedral : 4.331 43.297 1260 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.53 % Allowed : 26.34 % Favored : 71.12 % 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: 1.18 (0.26), residues: 1123 helix: 2.26 (0.25), residues: 443 sheet: 0.50 (0.33), residues: 240 loop : -0.58 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 164 HIS 0.005 0.001 HIS R 114 PHE 0.014 0.001 PHE R 327 TYR 0.024 0.001 TYR R 191 ARG 0.011 0.001 ARG R 51 *********************** 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 308 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 1.082 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8856 (mp0) cc_final: 0.8427 (mp0) REVERT: R 36 GLU cc_start: 0.8452 (tp30) cc_final: 0.7733 (tp30) REVERT: R 37 GLN cc_start: 0.9196 (tp40) cc_final: 0.8629 (tp-100) REVERT: R 39 PHE cc_start: 0.8887 (t80) cc_final: 0.8554 (t80) REVERT: R 40 LEU cc_start: 0.9326 (mm) cc_final: 0.9052 (tp) REVERT: R 43 ARG cc_start: 0.8822 (mmm160) cc_final: 0.8368 (mmm160) REVERT: R 47 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8671 (mm-40) REVERT: R 137 ASP cc_start: 0.8255 (m-30) cc_final: 0.8047 (m-30) REVERT: R 154 TRP cc_start: 0.6660 (m100) cc_final: 0.6429 (m100) REVERT: R 156 LEU cc_start: 0.7034 (mt) cc_final: 0.6359 (tt) REVERT: R 182 GLU cc_start: 0.7107 (tp30) cc_final: 0.6609 (tp30) REVERT: R 281 CYS cc_start: 0.4956 (OUTLIER) cc_final: 0.4686 (t) REVERT: R 374 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7364 (t0) REVERT: R 469 GLU cc_start: 0.7610 (tp30) cc_final: 0.7067 (tp30) REVERT: P 21 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8319 (tpp80) REVERT: A 27 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: A 29 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7801 (tm-30) REVERT: A 271 LYS cc_start: 0.8222 (mmtp) cc_final: 0.7939 (mttp) REVERT: A 311 TYR cc_start: 0.8197 (m-80) cc_final: 0.7929 (m-10) REVERT: A 381 ASP cc_start: 0.8276 (t0) cc_final: 0.8039 (t0) REVERT: B 12 GLU cc_start: 0.7800 (pp20) cc_final: 0.7128 (pp20) REVERT: B 22 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7832 (mtm180) REVERT: B 76 ASP cc_start: 0.8269 (p0) cc_final: 0.7849 (p0) REVERT: B 89 LYS cc_start: 0.8678 (mttp) cc_final: 0.8330 (mttp) REVERT: B 172 GLU cc_start: 0.7990 (tp30) cc_final: 0.7642 (tp30) REVERT: B 175 GLN cc_start: 0.8539 (tp40) cc_final: 0.7956 (mp10) REVERT: B 197 ARG cc_start: 0.7792 (tpp80) cc_final: 0.6863 (tpp80) REVERT: B 214 ARG cc_start: 0.7543 (ptp90) cc_final: 0.7226 (pmm-80) REVERT: B 219 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7837 (mmt-90) REVERT: B 234 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: B 258 ASP cc_start: 0.7966 (t0) cc_final: 0.6944 (t0) REVERT: G 18 GLN cc_start: 0.8665 (tp40) cc_final: 0.8395 (tp-100) REVERT: N 13 GLN cc_start: 0.8268 (pp30) cc_final: 0.7982 (mm-40) REVERT: N 35 ASN cc_start: 0.8728 (m-40) cc_final: 0.8485 (m-40) REVERT: N 53 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7279 (mp-120) REVERT: N 123 GLN cc_start: 0.8733 (tp40) cc_final: 0.8429 (tm-30) outliers start: 25 outliers final: 18 residues processed: 293 average time/residue: 1.5931 time to fit residues: 490.0718 Evaluate side-chains 298 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 374 ASN Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 118 ASP 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 53 GLN 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 64 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 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 R 374 ASN R 440 GLN P 5 HIS A 357 HIS B 17 GLN B 75 GLN N 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9389 Z= 0.218 Angle : 0.675 10.174 12708 Z= 0.340 Chirality : 0.043 0.218 1405 Planarity : 0.004 0.051 1617 Dihedral : 4.366 43.356 1260 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.53 % Allowed : 26.24 % Favored : 71.23 % 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: 2.21 (0.25), residues: 449 sheet: 0.54 (0.33), residues: 236 loop : -0.61 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 164 HIS 0.004 0.001 HIS R 114 PHE 0.014 0.001 PHE R 327 TYR 0.024 0.001 TYR R 191 ARG 0.015 0.001 ARG R 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 1.130 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: symmetry clash REVERT: R 35 GLU cc_start: 0.8848 (mp0) cc_final: 0.8427 (mp0) REVERT: R 36 GLU cc_start: 0.8460 (tp30) cc_final: 0.7751 (tp30) REVERT: R 37 GLN cc_start: 0.9208 (tp40) cc_final: 0.8649 (tp-100) REVERT: R 39 PHE cc_start: 0.8886 (t80) cc_final: 0.8550 (t80) REVERT: R 40 LEU cc_start: 0.9332 (mm) cc_final: 0.9057 (tp) REVERT: R 43 ARG cc_start: 0.8820 (mmm160) cc_final: 0.8367 (mmm160) REVERT: R 47 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8677 (mm-40) REVERT: R 154 TRP cc_start: 0.6658 (m100) cc_final: 0.6402 (m100) REVERT: R 156 LEU cc_start: 0.7021 (mt) cc_final: 0.6348 (tt) REVERT: R 182 GLU cc_start: 0.7129 (tp30) cc_final: 0.6633 (tp30) REVERT: R 281 CYS cc_start: 0.4884 (OUTLIER) cc_final: 0.4609 (t) REVERT: R 374 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7339 (t0) REVERT: R 405 LYS cc_start: 0.8465 (tppp) cc_final: 0.8249 (tppp) REVERT: R 469 GLU cc_start: 0.7628 (tp30) cc_final: 0.7088 (tp30) REVERT: P 21 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8335 (tpp80) REVERT: P 26 LYS cc_start: 0.8992 (tmmt) cc_final: 0.8653 (ttpp) REVERT: A 27 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: A 29 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7792 (tm-30) REVERT: A 311 TYR cc_start: 0.8180 (m-80) cc_final: 0.7914 (m-10) REVERT: A 381 ASP cc_start: 0.8277 (t0) cc_final: 0.8035 (t0) REVERT: B 76 ASP cc_start: 0.8283 (p0) cc_final: 0.7813 (p0) REVERT: B 89 LYS cc_start: 0.8681 (mttp) cc_final: 0.8360 (mttp) REVERT: B 172 GLU cc_start: 0.8014 (tp30) cc_final: 0.7673 (tp30) REVERT: B 197 ARG cc_start: 0.7795 (tpp80) cc_final: 0.6865 (tpp80) REVERT: B 214 ARG cc_start: 0.7512 (ptp90) cc_final: 0.7212 (pmm-80) REVERT: B 219 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7891 (mmm-85) REVERT: B 234 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: B 258 ASP cc_start: 0.7956 (t0) cc_final: 0.7610 (t0) REVERT: G 13 ARG cc_start: 0.8045 (mtt90) cc_final: 0.7621 (mpt180) REVERT: G 18 GLN cc_start: 0.8671 (tp40) cc_final: 0.8431 (tp-100) REVERT: N 13 GLN cc_start: 0.8267 (pp30) cc_final: 0.7959 (mm-40) REVERT: N 35 ASN cc_start: 0.8741 (m-40) cc_final: 0.8514 (m-40) REVERT: N 53 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7293 (mp-120) REVERT: N 115 TYR cc_start: 0.8873 (t80) cc_final: 0.8529 (t80) REVERT: N 123 GLN cc_start: 0.8742 (tp40) cc_final: 0.8429 (tm-30) outliers start: 25 outliers final: 17 residues processed: 283 average time/residue: 1.6116 time to fit residues: 479.3728 Evaluate side-chains 294 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 272 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 374 ASN Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 53 GLN 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 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 13 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- 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 R 374 ASN R 440 GLN A 357 HIS B 220 GLN N 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.103208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087462 restraints weight = 18064.688| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.70 r_work: 0.3161 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9389 Z= 0.200 Angle : 0.677 10.253 12708 Z= 0.342 Chirality : 0.043 0.212 1405 Planarity : 0.004 0.053 1617 Dihedral : 4.309 42.813 1260 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.33 % Allowed : 27.25 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1123 helix: 2.23 (0.25), residues: 449 sheet: 0.55 (0.33), residues: 236 loop : -0.61 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP R 164 HIS 0.012 0.001 HIS R 114 PHE 0.014 0.001 PHE A 212 TYR 0.024 0.001 TYR R 191 ARG 0.015 0.001 ARG R 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6564.87 seconds wall clock time: 116 minutes 42.64 seconds (7002.64 seconds total)