Starting phenix.real_space_refine on Thu Feb 5 04:42:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kbw_62232/02_2026/9kbw_62232_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kbw_62232/02_2026/9kbw_62232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kbw_62232/02_2026/9kbw_62232_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kbw_62232/02_2026/9kbw_62232_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kbw_62232/02_2026/9kbw_62232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kbw_62232/02_2026/9kbw_62232.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 55 5.16 5 C 4668 2.51 5 N 1276 2.21 5 O 1426 1.98 5 H 7179 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14613 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1187 Classifications: {'peptide': 72} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "B" Number of atoms: 6588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain: "C" Number of atoms: 6771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6771 Classifications: {'peptide': 439} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 260 SG CYS A 218 23.451 70.640 32.066 1.00165.25 S ATOM 1121 SG CYS A 270 24.972 71.883 34.826 1.00144.09 S Time building chain proxies: 2.48, per 1000 atoms: 0.17 Number of scatterers: 14613 At special positions: 0 Unit cell: (73.04, 84.66, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 55 16.00 P 6 15.00 Mg 2 11.99 O 1426 8.00 N 1276 7.00 C 4668 6.00 H 7179 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 345.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 218 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 270 " 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 7 sheets defined 51.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.690A pdb=" N LYS A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.697A pdb=" N MET A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 273' Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 49 removed outlier: 4.312A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.576A pdb=" N ASP B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.848A pdb=" N ILE B 86 " --> pdb=" O PHE B 83 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 87' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.887A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 148 through 161 removed outlier: 3.605A pdb=" N ILE B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.902A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.595A pdb=" N LEU B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.866A pdb=" N LEU B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.742A pdb=" N PHE B 244 " --> pdb=" O CYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.574A pdb=" N GLN B 282 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 284 " --> pdb=" O GLN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.532A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.532A pdb=" N VAL B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 400 removed outlier: 3.637A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.141A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 434 removed outlier: 3.982A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 removed outlier: 3.566A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.953A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.593A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.691A pdb=" N ASP C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 3.598A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.552A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.027A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.584A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 330 " --> pdb=" O LYS C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 400 removed outlier: 3.624A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.113A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 435 removed outlier: 3.864A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 228 removed outlier: 7.364A pdb=" N ARG A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 232 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE A 240 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.248A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B 140 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 139 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER B 374 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE B 319 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR B 376 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 317 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 378 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN B 380 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.806A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS C 200 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.806A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA7, first strand: chain 'C' and resid 269 through 272 removed outlier: 6.725A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 951 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: 2.65 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 7155 1.12 - 1.29: 1264 1.29 - 1.47: 2927 1.47 - 1.65: 3348 1.65 - 1.82: 86 Bond restraints: 14780 Sorted by residual: bond pdb=" N ASN C 186 " pdb=" H ASN C 186 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N LYS B 60 " pdb=" H LYS B 60 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NH2 ARG C 121 " pdb="HH22 ARG C 121 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" ND2 ASN B 249 " pdb="HD22 ASN B 249 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N CYS C 347 " pdb=" H CYS C 347 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 14775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 24347 3.58 - 7.16: 2148 7.16 - 10.74: 105 10.74 - 14.32: 20 14.32 - 17.90: 2 Bond angle restraints: 26622 Sorted by residual: angle pdb=" C THR B 287 " pdb=" N VAL B 288 " pdb=" CA VAL B 288 " ideal model delta sigma weight residual 120.24 125.68 -5.44 6.30e-01 2.52e+00 7.45e+01 angle pdb=" CA ASP B 69 " pdb=" CB ASP B 69 " pdb=" CG ASP B 69 " ideal model delta sigma weight residual 112.60 119.72 -7.12 1.00e+00 1.00e+00 5.07e+01 angle pdb=" C TYR C 262 " pdb=" N PRO C 263 " pdb=" CA PRO C 263 " ideal model delta sigma weight residual 119.47 127.61 -8.14 1.16e+00 7.43e-01 4.93e+01 angle pdb=" CA ASP C 392 " pdb=" CB ASP C 392 " pdb=" CG ASP C 392 " ideal model delta sigma weight residual 112.60 119.24 -6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" CD ARG B 48 " pdb=" NE ARG B 48 " pdb=" CZ ARG B 48 " ideal model delta sigma weight residual 124.40 132.81 -8.41 1.40e+00 5.10e-01 3.61e+01 ... (remaining 26617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 6624 35.08 - 70.17: 352 70.17 - 105.25: 15 105.25 - 140.34: 6 140.34 - 175.42: 3 Dihedral angle restraints: 7000 sinusoidal: 3799 harmonic: 3201 Sorted by residual: dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -79.99 -175.42 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -54.10 158.69 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -86.99 156.26 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 6997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 757 0.081 - 0.163: 273 0.163 - 0.244: 65 0.244 - 0.326: 24 0.326 - 0.407: 3 Chirality restraints: 1122 Sorted by residual: chirality pdb=" CA ARG B 215 " pdb=" N ARG B 215 " pdb=" C ARG B 215 " pdb=" CB ARG B 215 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA THR B 74 " pdb=" N THR B 74 " pdb=" C THR B 74 " pdb=" CB THR B 74 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA GLU C 207 " pdb=" N GLU C 207 " pdb=" C GLU C 207 " pdb=" CB GLU C 207 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 1119 not shown) Planarity restraints: 2233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 422 " -0.452 9.50e-02 1.11e+02 1.91e-01 3.33e+02 pdb=" NE ARG C 422 " -0.105 2.00e-02 2.50e+03 pdb=" CZ ARG C 422 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG C 422 " 0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG C 422 " 0.089 2.00e-02 2.50e+03 pdb="HH11 ARG C 422 " 0.162 2.00e-02 2.50e+03 pdb="HH12 ARG C 422 " -0.259 2.00e-02 2.50e+03 pdb="HH21 ARG C 422 " -0.033 2.00e-02 2.50e+03 pdb="HH22 ARG C 422 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 103 " 0.193 2.00e-02 2.50e+03 8.35e-02 2.09e+02 pdb=" CG TYR C 103 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR C 103 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR C 103 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR C 103 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR C 103 " -0.055 2.00e-02 2.50e+03 pdb=" CZ TYR C 103 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 103 " 0.162 2.00e-02 2.50e+03 pdb=" HD1 TYR C 103 " -0.086 2.00e-02 2.50e+03 pdb=" HD2 TYR C 103 " -0.033 2.00e-02 2.50e+03 pdb=" HE1 TYR C 103 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR C 103 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP B 501 " -0.187 2.00e-02 2.50e+03 8.26e-02 2.05e+02 pdb=" C2 GTP B 501 " -0.001 2.00e-02 2.50e+03 pdb=" C4 GTP B 501 " 0.039 2.00e-02 2.50e+03 pdb=" C5 GTP B 501 " 0.029 2.00e-02 2.50e+03 pdb=" C6 GTP B 501 " -0.036 2.00e-02 2.50e+03 pdb=" C8 GTP B 501 " 0.096 2.00e-02 2.50e+03 pdb=" N1 GTP B 501 " -0.077 2.00e-02 2.50e+03 pdb=" N2 GTP B 501 " 0.091 2.00e-02 2.50e+03 pdb=" N3 GTP B 501 " 0.051 2.00e-02 2.50e+03 pdb=" N7 GTP B 501 " 0.086 2.00e-02 2.50e+03 pdb=" N9 GTP B 501 " 0.009 2.00e-02 2.50e+03 pdb=" O6 GTP B 501 " -0.100 2.00e-02 2.50e+03 ... (remaining 2230 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 683 2.09 - 2.72: 21884 2.72 - 3.35: 43188 3.35 - 3.97: 58098 3.97 - 4.60: 85653 Nonbonded interactions: 209506 Sorted by model distance: nonbonded pdb=" OD1 ASP C 120 " pdb="HH21 ARG C 123 " model vdw 1.465 2.450 nonbonded pdb=" O ALA C 289 " pdb="HD21 ASN C 293 " model vdw 1.542 2.450 nonbonded pdb=" O ARG B 88 " pdb=" H ASP B 90 " model vdw 1.548 2.450 nonbonded pdb=" O ARG C 339 " pdb=" HG SER C 340 " model vdw 1.555 2.450 nonbonded pdb=" H ASP B 31 " pdb=" O SER B 35 " model vdw 1.578 2.450 ... (remaining 209501 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: 15.010 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: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 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 : 0.011 0.159 7603 Z= 0.632 Angle : 1.681 17.896 10316 Z= 1.090 Chirality : 0.093 0.407 1122 Planarity : 0.014 0.138 1343 Dihedral : 16.654 175.419 2802 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 1.00 % Allowed : 4.99 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.26), residues: 931 helix: -0.94 (0.23), residues: 403 sheet: 0.06 (0.42), residues: 135 loop : -1.23 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 264 TYR 0.161 0.016 TYR C 103 PHE 0.068 0.011 PHE C 296 TRP 0.101 0.023 TRP B 21 HIS 0.012 0.003 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.01043 ( 7601) covalent geometry : angle 1.68126 (10316) hydrogen bonds : bond 0.20046 ( 328) hydrogen bonds : angle 7.37570 ( 951) metal coordination : bond 0.11300 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 74 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 0.372 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: 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: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.4548 (mmm) cc_final: 0.4282 (mmm) REVERT: A 263 TYR cc_start: 0.6180 (t80) cc_final: 0.5626 (t80) REVERT: B 25 SER cc_start: 0.7582 (m) cc_final: 0.7143 (p) REVERT: B 86 ILE cc_start: 0.7199 (tt) cc_final: 0.6967 (tp) REVERT: B 166 MET cc_start: 0.6907 (mmm) cc_final: 0.6632 (tpp) REVERT: B 305 CYS cc_start: 0.6275 (p) cc_final: 0.6073 (p) REVERT: B 402 LYS cc_start: 0.6746 (mmtt) cc_final: 0.6380 (mttt) REVERT: C 109 THR cc_start: 0.7864 (m) cc_final: 0.6724 (m) REVERT: C 167 LEU cc_start: 0.7987 (mt) cc_final: 0.7581 (mp) outliers start: 8 outliers final: 3 residues processed: 226 average time/residue: 0.2590 time to fit residues: 73.8100 Evaluate side-chains 129 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 147 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 136 GLN B 247 GLN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS C 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.143008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.122900 restraints weight = 26670.128| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.92 r_work: 0.3860 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 7603 Z= 0.261 Angle : 0.748 7.651 10316 Z= 0.399 Chirality : 0.048 0.178 1122 Planarity : 0.006 0.072 1343 Dihedral : 14.905 176.974 1054 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 1.87 % Allowed : 9.86 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.26), residues: 931 helix: -0.25 (0.24), residues: 413 sheet: -0.65 (0.43), residues: 133 loop : -1.66 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 64 TYR 0.020 0.002 TYR C 24 PHE 0.033 0.003 PHE C 255 TRP 0.013 0.003 TRP C 21 HIS 0.009 0.002 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 7601) covalent geometry : angle 0.74762 (10316) hydrogen bonds : bond 0.05495 ( 328) hydrogen bonds : angle 5.27170 ( 951) metal coordination : bond 0.00539 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 74 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.6227 (mtmt) cc_final: 0.6007 (pttt) REVERT: A 250 MET cc_start: 0.5084 (mmm) cc_final: 0.4691 (mmm) REVERT: A 263 TYR cc_start: 0.6279 (t80) cc_final: 0.5728 (t80) REVERT: B 239 THR cc_start: 0.6931 (t) cc_final: 0.6653 (t) REVERT: C 269 LEU cc_start: 0.7904 (tt) cc_final: 0.7592 (mp) REVERT: C 306 ASP cc_start: 0.6402 (p0) cc_final: 0.6118 (p0) outliers start: 15 outliers final: 9 residues processed: 130 average time/residue: 0.1894 time to fit residues: 32.7691 Evaluate side-chains 104 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.141997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.121922 restraints weight = 26776.537| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.92 r_work: 0.3839 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7603 Z= 0.148 Angle : 0.585 5.463 10316 Z= 0.308 Chirality : 0.043 0.147 1122 Planarity : 0.005 0.068 1343 Dihedral : 12.919 168.449 1053 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.51 % Favored : 95.38 % Rotamer: Outliers : 1.62 % Allowed : 12.11 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.27), residues: 931 helix: 0.32 (0.25), residues: 414 sheet: -1.28 (0.41), residues: 134 loop : -1.42 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 271 TYR 0.009 0.001 TYR C 272 PHE 0.025 0.002 PHE C 255 TRP 0.010 0.002 TRP C 21 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7601) covalent geometry : angle 0.58462 (10316) hydrogen bonds : bond 0.04473 ( 328) hydrogen bonds : angle 4.86361 ( 951) metal coordination : bond 0.00151 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 74 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.6294 (mtmt) cc_final: 0.6061 (pttt) REVERT: A 250 MET cc_start: 0.4979 (mmm) cc_final: 0.4520 (mmm) REVERT: A 263 TYR cc_start: 0.6450 (t80) cc_final: 0.5802 (t80) REVERT: B 113 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6728 (mp0) REVERT: B 429 VAL cc_start: 0.7049 (t) cc_final: 0.6692 (p) REVERT: C 269 LEU cc_start: 0.7896 (tt) cc_final: 0.7661 (mp) REVERT: C 306 ASP cc_start: 0.6538 (p0) cc_final: 0.6328 (p0) REVERT: C 357 TYR cc_start: 0.7144 (m-10) cc_final: 0.6878 (m-80) REVERT: C 425 MET cc_start: 0.7315 (tpp) cc_final: 0.7081 (tpp) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.2087 time to fit residues: 29.4618 Evaluate side-chains 103 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 255 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 87 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.138431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.118688 restraints weight = 27146.948| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.91 r_work: 0.3789 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 7603 Z= 0.203 Angle : 0.625 5.815 10316 Z= 0.331 Chirality : 0.045 0.165 1122 Planarity : 0.005 0.071 1343 Dihedral : 12.681 171.153 1053 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.83 % Favored : 95.06 % Rotamer: Outliers : 2.62 % Allowed : 13.11 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.26), residues: 931 helix: 0.19 (0.25), residues: 418 sheet: -1.77 (0.40), residues: 134 loop : -1.63 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 215 TYR 0.011 0.002 TYR B 53 PHE 0.031 0.002 PHE C 255 TRP 0.012 0.002 TRP C 21 HIS 0.008 0.002 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 7601) covalent geometry : angle 0.62494 (10316) hydrogen bonds : bond 0.04732 ( 328) hydrogen bonds : angle 4.91238 ( 951) metal coordination : bond 0.00194 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 74 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 TYR cc_start: 0.6587 (t80) cc_final: 0.5723 (t80) REVERT: B 93 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7840 (p) REVERT: B 113 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6876 (mp0) REVERT: B 429 VAL cc_start: 0.7062 (t) cc_final: 0.6729 (p) REVERT: C 155 GLU cc_start: 0.7204 (tt0) cc_final: 0.6959 (tt0) REVERT: C 254 GLU cc_start: 0.2772 (tp30) cc_final: 0.2445 (mm-30) REVERT: C 306 ASP cc_start: 0.6370 (p0) cc_final: 0.6149 (p0) REVERT: C 357 TYR cc_start: 0.7258 (m-10) cc_final: 0.6934 (m-80) REVERT: C 425 MET cc_start: 0.7416 (tpp) cc_final: 0.7170 (tpp) outliers start: 21 outliers final: 13 residues processed: 113 average time/residue: 0.2001 time to fit residues: 29.8027 Evaluate side-chains 107 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.136450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.116773 restraints weight = 27692.968| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.92 r_work: 0.3764 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 7603 Z= 0.247 Angle : 0.664 7.393 10316 Z= 0.353 Chirality : 0.046 0.165 1122 Planarity : 0.006 0.073 1343 Dihedral : 13.085 169.950 1052 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.12 % Allowed : 14.48 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.26), residues: 931 helix: 0.05 (0.25), residues: 409 sheet: -2.29 (0.41), residues: 124 loop : -1.67 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 88 TYR 0.010 0.002 TYR B 53 PHE 0.035 0.003 PHE C 255 TRP 0.013 0.002 TRP C 21 HIS 0.008 0.002 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 7601) covalent geometry : angle 0.66404 (10316) hydrogen bonds : bond 0.05042 ( 328) hydrogen bonds : angle 5.19956 ( 951) metal coordination : bond 0.00168 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 74 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.4130 (t80) cc_final: 0.3910 (t80) REVERT: A 263 TYR cc_start: 0.6599 (t80) cc_final: 0.6346 (t80) REVERT: B 113 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6871 (mp0) REVERT: B 145 THR cc_start: 0.4610 (OUTLIER) cc_final: 0.4032 (t) REVERT: C 90 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6587 (mp0) REVERT: C 254 GLU cc_start: 0.2840 (tp30) cc_final: 0.2529 (mm-30) REVERT: C 357 TYR cc_start: 0.7354 (m-10) cc_final: 0.7024 (m-80) outliers start: 25 outliers final: 18 residues processed: 111 average time/residue: 0.1796 time to fit residues: 26.7859 Evaluate side-chains 107 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 0.0060 chunk 2 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.139032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.119316 restraints weight = 27247.850| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.92 r_work: 0.3813 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.6832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7603 Z= 0.135 Angle : 0.563 5.729 10316 Z= 0.295 Chirality : 0.042 0.154 1122 Planarity : 0.005 0.070 1343 Dihedral : 12.374 168.792 1052 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.37 % Allowed : 16.48 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.27), residues: 931 helix: 0.58 (0.26), residues: 406 sheet: -1.90 (0.42), residues: 129 loop : -1.31 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 284 TYR 0.019 0.001 TYR B 161 PHE 0.024 0.002 PHE C 255 TRP 0.013 0.002 TRP C 21 HIS 0.006 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7601) covalent geometry : angle 0.56319 (10316) hydrogen bonds : bond 0.03986 ( 328) hydrogen bonds : angle 4.82754 ( 951) metal coordination : bond 0.00060 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 74 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.6358 (mtmt) cc_final: 0.6096 (pttt) REVERT: A 222 PHE cc_start: 0.4056 (t80) cc_final: 0.3830 (t80) REVERT: A 263 TYR cc_start: 0.6611 (t80) cc_final: 0.6339 (t80) REVERT: B 113 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6814 (mp0) REVERT: B 145 THR cc_start: 0.4724 (OUTLIER) cc_final: 0.4171 (t) REVERT: B 372 LYS cc_start: 0.7597 (mmtm) cc_final: 0.7097 (tttp) REVERT: C 90 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6339 (mm-30) REVERT: C 357 TYR cc_start: 0.7217 (m-10) cc_final: 0.6876 (m-80) outliers start: 19 outliers final: 13 residues processed: 105 average time/residue: 0.2063 time to fit residues: 28.5202 Evaluate side-chains 102 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 192 HIS ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.135394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.116244 restraints weight = 27740.119| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.84 r_work: 0.3774 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 7603 Z= 0.230 Angle : 0.638 6.759 10316 Z= 0.340 Chirality : 0.045 0.155 1122 Planarity : 0.006 0.073 1343 Dihedral : 12.902 170.346 1052 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.12 % Allowed : 16.23 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.27), residues: 931 helix: 0.37 (0.25), residues: 400 sheet: -2.05 (0.42), residues: 130 loop : -1.53 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 284 TYR 0.016 0.002 TYR B 161 PHE 0.032 0.002 PHE C 255 TRP 0.012 0.002 TRP C 21 HIS 0.008 0.002 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 7601) covalent geometry : angle 0.63763 (10316) hydrogen bonds : bond 0.04796 ( 328) hydrogen bonds : angle 5.08469 ( 951) metal coordination : bond 0.00128 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 74 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 263 TYR cc_start: 0.6578 (t80) cc_final: 0.6229 (t80) REVERT: A 265 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7158 (pp) REVERT: B 75 MET cc_start: 0.7672 (mmt) cc_final: 0.7338 (mmt) REVERT: B 113 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6815 (mp0) REVERT: B 145 THR cc_start: 0.4873 (OUTLIER) cc_final: 0.4292 (t) REVERT: C 90 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6515 (mp0) REVERT: C 378 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8171 (pp) outliers start: 25 outliers final: 21 residues processed: 104 average time/residue: 0.1984 time to fit residues: 27.6971 Evaluate side-chains 108 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.139458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.120072 restraints weight = 27390.961| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.90 r_work: 0.3806 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7603 Z= 0.120 Angle : 0.552 5.681 10316 Z= 0.287 Chirality : 0.042 0.156 1122 Planarity : 0.005 0.071 1343 Dihedral : 12.234 168.651 1052 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.87 % Allowed : 17.10 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.28), residues: 931 helix: 0.90 (0.26), residues: 400 sheet: -2.06 (0.43), residues: 136 loop : -1.19 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.014 0.001 TYR B 161 PHE 0.021 0.001 PHE C 255 TRP 0.041 0.003 TRP B 346 HIS 0.006 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7601) covalent geometry : angle 0.55174 (10316) hydrogen bonds : bond 0.03734 ( 328) hydrogen bonds : angle 4.70778 ( 951) metal coordination : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 74 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.6426 (mtmt) cc_final: 0.6146 (pttt) REVERT: A 222 PHE cc_start: 0.3962 (t80) cc_final: 0.3696 (t80) REVERT: A 263 TYR cc_start: 0.6549 (t80) cc_final: 0.6205 (t80) REVERT: B 75 MET cc_start: 0.7624 (mmt) cc_final: 0.7348 (mmt) REVERT: B 86 ILE cc_start: 0.7287 (tt) cc_final: 0.7020 (tt) REVERT: B 113 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6856 (mp0) REVERT: B 145 THR cc_start: 0.4825 (OUTLIER) cc_final: 0.4545 (t) REVERT: B 372 LYS cc_start: 0.7637 (mmtm) cc_final: 0.7065 (tttp) outliers start: 15 outliers final: 13 residues processed: 104 average time/residue: 0.1862 time to fit residues: 25.6324 Evaluate side-chains 101 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 378 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.138864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.119557 restraints weight = 27520.666| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.86 r_work: 0.3805 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.7174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7603 Z= 0.129 Angle : 0.551 5.594 10316 Z= 0.286 Chirality : 0.042 0.150 1122 Planarity : 0.005 0.071 1343 Dihedral : 12.168 168.382 1052 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.00 % Allowed : 17.48 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.28), residues: 931 helix: 1.00 (0.26), residues: 400 sheet: -2.02 (0.43), residues: 136 loop : -1.15 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 284 TYR 0.013 0.001 TYR B 161 PHE 0.022 0.002 PHE C 255 TRP 0.037 0.002 TRP B 346 HIS 0.005 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7601) covalent geometry : angle 0.55130 (10316) hydrogen bonds : bond 0.03787 ( 328) hydrogen bonds : angle 4.62352 ( 951) metal coordination : bond 0.00122 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 74 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 208 LYS cc_start: 0.6384 (mtmt) cc_final: 0.6105 (pttt) REVERT: A 222 PHE cc_start: 0.3905 (t80) cc_final: 0.3652 (t80) REVERT: A 263 TYR cc_start: 0.6432 (t80) cc_final: 0.6072 (t80) REVERT: B 86 ILE cc_start: 0.7295 (tt) cc_final: 0.7016 (tt) REVERT: B 113 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6841 (mp0) REVERT: B 145 THR cc_start: 0.5139 (OUTLIER) cc_final: 0.4499 (t) REVERT: B 372 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7046 (tttp) REVERT: C 90 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6754 (mm-30) outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.2071 time to fit residues: 27.9302 Evaluate side-chains 105 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.136089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.117118 restraints weight = 27827.774| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.84 r_work: 0.3784 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.7330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 7603 Z= 0.212 Angle : 0.621 6.507 10316 Z= 0.329 Chirality : 0.045 0.154 1122 Planarity : 0.006 0.076 1343 Dihedral : 12.758 170.402 1052 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.00 % Allowed : 17.60 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.28), residues: 931 helix: 0.68 (0.26), residues: 400 sheet: -2.17 (0.42), residues: 137 loop : -1.31 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 284 TYR 0.013 0.002 TYR B 161 PHE 0.029 0.002 PHE C 255 TRP 0.033 0.003 TRP B 346 HIS 0.007 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 7601) covalent geometry : angle 0.62091 (10316) hydrogen bonds : bond 0.04609 ( 328) hydrogen bonds : angle 4.96493 ( 951) metal coordination : bond 0.00170 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 74 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.5385 (mmm) cc_final: 0.5102 (mmm) REVERT: A 263 TYR cc_start: 0.6615 (t80) cc_final: 0.6131 (t80) REVERT: B 113 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6790 (mp0) REVERT: B 145 THR cc_start: 0.5581 (OUTLIER) cc_final: 0.5224 (t) REVERT: B 372 LYS cc_start: 0.7701 (mmtm) cc_final: 0.7118 (tttp) outliers start: 16 outliers final: 13 residues processed: 106 average time/residue: 0.2173 time to fit residues: 30.0474 Evaluate side-chains 107 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 396 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.138258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.118671 restraints weight = 27583.865| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.94 r_work: 0.3793 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.7340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7603 Z= 0.134 Angle : 0.557 5.648 10316 Z= 0.290 Chirality : 0.042 0.150 1122 Planarity : 0.005 0.073 1343 Dihedral : 12.245 168.617 1052 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.87 % Allowed : 17.73 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.28), residues: 931 helix: 0.97 (0.27), residues: 400 sheet: -2.13 (0.43), residues: 136 loop : -1.17 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 284 TYR 0.013 0.001 TYR B 161 PHE 0.021 0.002 PHE C 255 TRP 0.035 0.002 TRP B 346 HIS 0.007 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7601) covalent geometry : angle 0.55744 (10316) hydrogen bonds : bond 0.03829 ( 328) hydrogen bonds : angle 4.70820 ( 951) metal coordination : bond 0.00085 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3768.25 seconds wall clock time: 64 minutes 48.54 seconds (3888.54 seconds total)