Starting phenix.real_space_refine on Sat Aug 23 13:20:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvu_17972/08_2025/8pvu_17972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvu_17972/08_2025/8pvu_17972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pvu_17972/08_2025/8pvu_17972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvu_17972/08_2025/8pvu_17972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pvu_17972/08_2025/8pvu_17972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvu_17972/08_2025/8pvu_17972.map" } resolution = 3.5 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= 0.036 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 68 5.16 5 C 7887 2.51 5 N 2101 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12336 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2480 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 16, 'TRANS': 284} Chain breaks: 5 Chain: "A" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2586 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2487 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2409 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 3 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2374 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 13, 'TRANS': 289} Chain breaks: 3 Time building chain proxies: 3.24, per 1000 atoms: 0.26 Number of scatterers: 12336 At special positions: 0 Unit cell: (91.16, 97.18, 137.6, 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 68 16.00 O 2280 8.00 N 2101 7.00 C 7887 6.00 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: 1.04 Conformation dependent library (CDL) restraints added in 586.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2902 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 10 sheets defined 54.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'E' and resid 61 through 78 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 122 through 143 Processing helix chain 'E' and resid 151 through 153 No H-bonds generated for 'chain 'E' and resid 151 through 153' Processing helix chain 'E' and resid 195 through 200 Processing helix chain 'E' and resid 207 through 223 removed outlier: 4.170A pdb=" N ILE E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 257 through 266 Processing helix chain 'E' and resid 274 through 279 removed outlier: 3.617A pdb=" N LEU E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 294 Processing helix chain 'E' and resid 303 through 309 Processing helix chain 'E' and resid 340 through 352 Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.803A pdb=" N GLY A 50 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 52 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 74 removed outlier: 3.951A pdb=" N ASN A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A 73 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.788A pdb=" N ILE A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 109' Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.988A pdb=" N HIS A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.516A pdb=" N VAL A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.872A pdb=" N GLU A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 197 removed outlier: 4.035A pdb=" N PHE A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP A 181 " --> pdb=" O CYS A 177 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.554A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 removed outlier: 3.798A pdb=" N TRP A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN A 225 " --> pdb=" O TYR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.635A pdb=" N ASP A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 3.851A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 removed outlier: 3.505A pdb=" N HIS A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.804A pdb=" N ALA A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 345 Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.874A pdb=" N GLU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.709A pdb=" N ARG B 38 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.635A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 53 removed outlier: 4.681A pdb=" N GLY B 53 " --> pdb=" O GLY B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 53' Processing helix chain 'B' and resid 54 through 74 removed outlier: 3.696A pdb=" N ASN B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 4.116A pdb=" N ILE B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 removed outlier: 3.925A pdb=" N HIS B 122 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 141 removed outlier: 4.185A pdb=" N GLU B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 173 through 196 removed outlier: 3.883A pdb=" N CYS B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 179 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 180 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 181 " --> pdb=" O CYS B 177 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.649A pdb=" N GLN B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 removed outlier: 3.672A pdb=" N GLU B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.907A pdb=" N TRP B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 225 " --> pdb=" O TYR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 removed outlier: 4.068A pdb=" N GLY B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.811A pdb=" N ALA B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 295 through 298 Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 342 through 353 removed outlier: 3.715A pdb=" N VAL B 346 " --> pdb=" O ASP B 342 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Proline residue: B 348 - end of helix removed outlier: 3.544A pdb=" N GLU B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.584A pdb=" N ARG C 38 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.506A pdb=" N GLU C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 56 through 74 Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.923A pdb=" N ILE C 108 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 109' Processing helix chain 'C' and resid 112 through 122 removed outlier: 3.843A pdb=" N HIS C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 removed outlier: 3.589A pdb=" N VAL C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C 138 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.799A pdb=" N GLU C 160 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 197 removed outlier: 4.162A pdb=" N LYS C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 179 " --> pdb=" O ASN C 175 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 3.898A pdb=" N ASP C 188 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 removed outlier: 3.697A pdb=" N GLU C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.673A pdb=" N GLN C 225 " --> pdb=" O TYR C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 248 removed outlier: 3.773A pdb=" N ASP C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 removed outlier: 3.767A pdb=" N LEU C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 296 removed outlier: 3.661A pdb=" N HIS C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N MET C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.510A pdb=" N VAL C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) Proline residue: C 348 - end of helix removed outlier: 3.571A pdb=" N GLU C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.761A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 56 through 75 removed outlier: 3.554A pdb=" N GLU D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 4.118A pdb=" N ILE D 108 " --> pdb=" O THR D 104 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 removed outlier: 4.415A pdb=" N THR D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS D 122 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 removed outlier: 3.944A pdb=" N GLU D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 198 removed outlier: 3.860A pdb=" N LYS D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 180 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Proline residue: D 185 - end of helix removed outlier: 3.554A pdb=" N GLN D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.844A pdb=" N LYS D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 226 removed outlier: 3.579A pdb=" N TRP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS D 226 " --> pdb=" O TYR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 252 removed outlier: 4.130A pdb=" N GLY D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS D 248 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR D 250 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 272 removed outlier: 3.661A pdb=" N LEU D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 removed outlier: 3.790A pdb=" N HIS D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 327 removed outlier: 4.093A pdb=" N ALA D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL D 325 " --> pdb=" O PRO D 321 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 320 through 327' Processing helix chain 'D' and resid 346 through 354 Processing sheet with id=AA1, first strand: chain 'E' and resid 25 through 26 removed outlier: 3.677A pdb=" N VAL E 49 " --> pdb=" O ASP E 44 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP E 88 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AA3, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 232 removed outlier: 6.576A pdb=" N LEU A 128 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 127 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 302 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 303 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N VAL A 339 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR A 305 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 232 removed outlier: 6.588A pdb=" N LEU B 128 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 99 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL B 129 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 101 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 98 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE B 279 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE B 100 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU B 281 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY B 102 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 302 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA B 303 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N VAL B 339 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR B 305 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 148 Processing sheet with id=AA8, first strand: chain 'C' and resid 231 through 232 removed outlier: 6.533A pdb=" N LEU C 128 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 99 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N VAL C 129 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 101 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR C 302 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA C 303 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL C 339 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR C 305 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 163 through 166 Processing sheet with id=AB1, first strand: chain 'D' and resid 231 through 232 removed outlier: 6.864A pdb=" N LEU D 128 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N VAL D 127 " --> pdb=" O CYS D 97 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE D 99 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N VAL D 129 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU D 101 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR D 302 " --> pdb=" O THR D 276 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2882 1.33 - 1.45: 2535 1.45 - 1.57: 7056 1.57 - 1.69: 0 1.69 - 1.81: 113 Bond restraints: 12586 Sorted by residual: bond pdb=" N ILE D 330 " pdb=" CA ILE D 330 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.18e+01 bond pdb=" N ILE E 324 " pdb=" CA ILE E 324 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" N GLY D 299 " pdb=" CA GLY D 299 " ideal model delta sigma weight residual 1.446 1.477 -0.032 1.02e-02 9.61e+03 9.54e+00 bond pdb=" N ILE E 255 " pdb=" CA ILE E 255 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.27e-02 6.20e+03 9.04e+00 bond pdb=" C SER E 246 " pdb=" N PRO E 247 " ideal model delta sigma weight residual 1.335 1.361 -0.026 8.70e-03 1.32e+04 8.77e+00 ... (remaining 12581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 16604 2.09 - 4.18: 401 4.18 - 6.27: 36 6.27 - 8.36: 4 8.36 - 10.45: 2 Bond angle restraints: 17047 Sorted by residual: angle pdb=" CA GLY D 299 " pdb=" C GLY D 299 " pdb=" O GLY D 299 " ideal model delta sigma weight residual 122.23 118.51 3.72 6.90e-01 2.10e+00 2.91e+01 angle pdb=" N ALA E 143 " pdb=" CA ALA E 143 " pdb=" C ALA E 143 " ideal model delta sigma weight residual 113.01 107.81 5.20 1.20e+00 6.94e-01 1.88e+01 angle pdb=" CA PRO E 196 " pdb=" N PRO E 196 " pdb=" CD PRO E 196 " ideal model delta sigma weight residual 112.00 106.32 5.68 1.40e+00 5.10e-01 1.64e+01 angle pdb=" CA LEU E 252 " pdb=" C LEU E 252 " pdb=" O LEU E 252 " ideal model delta sigma weight residual 122.64 117.83 4.81 1.25e+00 6.40e-01 1.48e+01 angle pdb=" N GLN E 66 " pdb=" CA GLN E 66 " pdb=" C GLN E 66 " ideal model delta sigma weight residual 111.28 107.17 4.11 1.09e+00 8.42e-01 1.42e+01 ... (remaining 17042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6369 17.96 - 35.92: 829 35.92 - 53.88: 275 53.88 - 71.84: 44 71.84 - 89.80: 12 Dihedral angle restraints: 7529 sinusoidal: 3023 harmonic: 4506 Sorted by residual: dihedral pdb=" CA LEU E 338 " pdb=" C LEU E 338 " pdb=" N PRO E 339 " pdb=" CA PRO E 339 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CG ARG C 38 " pdb=" CD ARG C 38 " pdb=" NE ARG C 38 " pdb=" CZ ARG C 38 " ideal model delta sinusoidal sigma weight residual 90.00 42.56 47.44 2 1.50e+01 4.44e-03 1.16e+01 dihedral pdb=" CB GLU E 71 " pdb=" CG GLU E 71 " pdb=" CD GLU E 71 " pdb=" OE1 GLU E 71 " ideal model delta sinusoidal sigma weight residual 0.00 -89.77 89.77 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1378 0.046 - 0.092: 371 0.092 - 0.138: 144 0.138 - 0.183: 15 0.183 - 0.229: 8 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CB THR D 268 " pdb=" CA THR D 268 " pdb=" OG1 THR D 268 " pdb=" CG2 THR D 268 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO E 196 " pdb=" N PRO E 196 " pdb=" C PRO E 196 " pdb=" CB PRO E 196 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE E 72 " pdb=" N ILE E 72 " pdb=" C ILE E 72 " pdb=" CB ILE E 72 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1913 not shown) Planarity restraints: 2192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 195 " -0.064 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO E 196 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 338 " -0.045 5.00e-02 4.00e+02 6.94e-02 7.71e+00 pdb=" N PRO E 339 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO E 339 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 339 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 201 " 0.013 2.00e-02 2.50e+03 1.56e-02 6.08e+00 pdb=" CG TRP C 201 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 201 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 201 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 201 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 201 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 201 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 201 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 201 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 201 " 0.003 2.00e-02 2.50e+03 ... (remaining 2189 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2335 2.77 - 3.30: 11593 3.30 - 3.83: 18844 3.83 - 4.37: 21072 4.37 - 4.90: 35967 Nonbonded interactions: 89811 Sorted by model distance: nonbonded pdb=" O GLU A 323 " pdb=" OG SER A 326 " model vdw 2.234 3.040 nonbonded pdb=" O GLU A 174 " pdb=" NZ LYS A 178 " model vdw 2.244 3.120 nonbonded pdb=" O GLY B 50 " pdb=" OG1 THR B 57 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASP C 258 " pdb=" N ILE C 259 " model vdw 2.273 3.120 nonbonded pdb=" O LYS C 200 " pdb=" NZ LYS C 205 " model vdw 2.283 3.120 ... (remaining 89806 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 74 or resid 93 through 148 or resid 164 through \ 314 or resid 323 through 359)) selection = (chain 'B' and (resid 29 through 74 or resid 93 through 148 or resid 164 through \ 314 or resid 323 through 359)) selection = (chain 'C' and (resid 29 through 148 or resid 164 through 314 or resid 323 throu \ gh 359)) selection = (chain 'D' and (resid 29 through 74 or resid 93 through 314 or resid 323 through \ 359)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.620 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.005 0.063 12586 Z= 0.282 Angle : 0.705 10.455 17047 Z= 0.449 Chirality : 0.049 0.229 1916 Planarity : 0.005 0.094 2192 Dihedral : 18.071 89.799 4627 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.09 % Allowed : 32.16 % Favored : 65.74 % 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 aren not related in a simple way. whole: -0.08 (0.22), residues: 1520 helix: 0.44 (0.21), residues: 616 sheet: 0.97 (0.44), residues: 157 loop : -0.64 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 117 TYR 0.034 0.001 TYR E 193 PHE 0.017 0.002 PHE C 246 TRP 0.040 0.002 TRP C 201 HIS 0.004 0.001 HIS E 80 Details of bonding type rmsd covalent geometry : bond 0.00468 (12586) covalent geometry : angle 0.70515 (17047) hydrogen bonds : bond 0.25767 ( 454) hydrogen bonds : angle 6.80988 ( 1302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 556 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 135 ARG cc_start: 0.7752 (ttt180) cc_final: 0.7544 (ttt90) REVERT: E 138 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8266 (ttpt) REVERT: E 194 ARG cc_start: 0.7203 (mtp-110) cc_final: 0.6770 (mtp-110) REVERT: E 308 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8246 (mt) REVERT: E 316 TYR cc_start: 0.7769 (m-10) cc_final: 0.7455 (m-10) REVERT: E 322 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: E 324 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6771 (pp) REVERT: A 124 MET cc_start: 0.7692 (mmt) cc_final: 0.7442 (mmt) REVERT: A 175 ASN cc_start: 0.8018 (m-40) cc_final: 0.7748 (m-40) REVERT: A 187 LEU cc_start: 0.8341 (mm) cc_final: 0.8031 (mp) REVERT: A 212 LYS cc_start: 0.8368 (mmmm) cc_final: 0.8145 (mtpp) REVERT: A 246 PHE cc_start: 0.8442 (t80) cc_final: 0.8091 (t80) REVERT: A 248 HIS cc_start: 0.8690 (t-90) cc_final: 0.8392 (t-170) REVERT: A 353 GLU cc_start: 0.7351 (mp0) cc_final: 0.7144 (mp0) REVERT: B 157 GLU cc_start: 0.7473 (tt0) cc_final: 0.7157 (tp30) REVERT: B 193 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 200 LYS cc_start: 0.8530 (mptt) cc_final: 0.8321 (mptt) REVERT: C 338 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7392 (tmmt) REVERT: D 184 MET cc_start: 0.7774 (mpp) cc_final: 0.7406 (mpp) REVERT: D 353 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6958 (tm-30) outliers start: 28 outliers final: 11 residues processed: 572 average time/residue: 0.1371 time to fit residues: 107.1991 Evaluate side-chains 567 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 551 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 331 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 253 ASN A 67 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN C 121 GLN C 123 ASN D 37 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107102 restraints weight = 19815.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111176 restraints weight = 8989.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113871 restraints weight = 5115.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115635 restraints weight = 3391.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116920 restraints weight = 2517.746| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12586 Z= 0.213 Angle : 0.576 8.763 17047 Z= 0.310 Chirality : 0.045 0.165 1916 Planarity : 0.005 0.059 2192 Dihedral : 6.773 69.342 1721 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.16 % Allowed : 28.27 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1520 helix: 0.56 (0.20), residues: 663 sheet: 1.04 (0.44), residues: 161 loop : -0.77 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 38 TYR 0.022 0.001 TYR E 233 PHE 0.019 0.002 PHE D 100 TRP 0.018 0.001 TRP B 201 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00466 (12586) covalent geometry : angle 0.57615 (17047) hydrogen bonds : bond 0.06054 ( 454) hydrogen bonds : angle 4.83314 ( 1302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 582 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4169 (OUTLIER) cc_final: 0.1764 (p90) REVERT: E 60 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6537 (pm20) REVERT: E 146 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7243 (tt) REVERT: E 194 ARG cc_start: 0.7180 (mtp-110) cc_final: 0.6706 (mtp-110) REVERT: E 308 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7867 (tp) REVERT: E 316 TYR cc_start: 0.7834 (m-10) cc_final: 0.7482 (m-10) REVERT: E 324 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6735 (pp) REVERT: A 67 ASN cc_start: 0.8573 (t0) cc_final: 0.8284 (t0) REVERT: A 124 MET cc_start: 0.7739 (mmt) cc_final: 0.7370 (mmt) REVERT: A 175 ASN cc_start: 0.8131 (m-40) cc_final: 0.7833 (m-40) REVERT: A 178 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7463 (mtmm) REVERT: A 329 LYS cc_start: 0.8178 (mttt) cc_final: 0.7727 (mttt) REVERT: A 353 GLU cc_start: 0.7519 (mp0) cc_final: 0.7292 (mp0) REVERT: B 32 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6991 (ttp80) REVERT: B 157 GLU cc_start: 0.7422 (tt0) cc_final: 0.7125 (tp30) REVERT: B 200 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8306 (mptt) REVERT: B 218 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 308 THR cc_start: 0.8670 (t) cc_final: 0.8455 (p) REVERT: C 43 ARG cc_start: 0.7471 (tmm160) cc_final: 0.7135 (tmm160) REVERT: C 64 GLN cc_start: 0.7997 (tp40) cc_final: 0.7616 (tp40) REVERT: C 103 TYR cc_start: 0.8482 (p90) cc_final: 0.7809 (p90) REVERT: C 199 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8345 (t) REVERT: C 206 MET cc_start: 0.7845 (ttp) cc_final: 0.7585 (ttp) REVERT: C 215 ASN cc_start: 0.8278 (t0) cc_final: 0.7961 (t0) REVERT: C 354 THR cc_start: 0.7746 (p) cc_final: 0.7514 (p) REVERT: D 99 ILE cc_start: 0.7977 (tt) cc_final: 0.7600 (tp) REVERT: D 114 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6872 (mm-30) REVERT: D 116 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8557 (tt) REVERT: D 117 ARG cc_start: 0.8662 (tmm-80) cc_final: 0.8456 (tmm-80) REVERT: D 166 ILE cc_start: 0.6149 (OUTLIER) cc_final: 0.5840 (mp) REVERT: D 179 PHE cc_start: 0.8707 (t80) cc_final: 0.8414 (t80) REVERT: D 338 LYS cc_start: 0.7361 (pttm) cc_final: 0.6977 (pttm) REVERT: D 353 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7051 (tm-30) outliers start: 69 outliers final: 35 residues processed: 611 average time/residue: 0.1305 time to fit residues: 110.3550 Evaluate side-chains 628 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 584 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 116 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 0.0070 chunk 59 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 109 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 GLN A 194 GLN B 55 GLN B 58 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN C 227 ASN D 30 GLN D 37 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110195 restraints weight = 19970.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114348 restraints weight = 9058.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117029 restraints weight = 5126.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118913 restraints weight = 3400.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120209 restraints weight = 2480.874| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12586 Z= 0.100 Angle : 0.488 9.267 17047 Z= 0.254 Chirality : 0.041 0.161 1916 Planarity : 0.004 0.054 2192 Dihedral : 4.898 57.197 1693 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.09 % Allowed : 29.47 % Favored : 65.45 % 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 aren not related in a simple way. whole: 0.21 (0.22), residues: 1520 helix: 0.77 (0.20), residues: 669 sheet: 1.59 (0.45), residues: 149 loop : -0.78 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 264 TYR 0.021 0.001 TYR A 118 PHE 0.011 0.001 PHE D 312 TRP 0.014 0.001 TRP C 201 HIS 0.005 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00227 (12586) covalent geometry : angle 0.48767 (17047) hydrogen bonds : bond 0.03754 ( 454) hydrogen bonds : angle 4.18295 ( 1302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 540 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4156 (OUTLIER) cc_final: 0.1794 (p90) REVERT: E 60 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6344 (pm20) REVERT: E 210 ASP cc_start: 0.7871 (m-30) cc_final: 0.7640 (m-30) REVERT: E 308 LEU cc_start: 0.8230 (tp) cc_final: 0.7857 (tt) REVERT: E 316 TYR cc_start: 0.7786 (m-10) cc_final: 0.7463 (m-10) REVERT: E 324 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6726 (pp) REVERT: A 124 MET cc_start: 0.7716 (mmt) cc_final: 0.7418 (mmt) REVERT: A 175 ASN cc_start: 0.8071 (m-40) cc_final: 0.7724 (m-40) REVERT: A 178 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7379 (mtmm) REVERT: A 329 LYS cc_start: 0.8145 (mttt) cc_final: 0.7559 (mttt) REVERT: B 157 GLU cc_start: 0.7447 (tt0) cc_final: 0.7137 (tp30) REVERT: C 34 TYR cc_start: 0.7805 (t80) cc_final: 0.7389 (t80) REVERT: C 43 ARG cc_start: 0.7417 (tmm160) cc_final: 0.6922 (tmm160) REVERT: C 64 GLN cc_start: 0.7984 (tp40) cc_final: 0.7660 (tp40) REVERT: C 103 TYR cc_start: 0.8449 (p90) cc_final: 0.8065 (p90) REVERT: C 199 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8362 (t) REVERT: C 206 MET cc_start: 0.7930 (ttt) cc_final: 0.7604 (ttp) REVERT: C 215 ASN cc_start: 0.8376 (t0) cc_final: 0.7933 (t0) REVERT: C 338 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7457 (tmmt) REVERT: C 354 THR cc_start: 0.7574 (p) cc_final: 0.7353 (p) REVERT: D 38 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7734 (mtp180) REVERT: D 99 ILE cc_start: 0.7765 (tt) cc_final: 0.7290 (tp) REVERT: D 114 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6788 (mm-30) REVERT: D 179 PHE cc_start: 0.8785 (t80) cc_final: 0.8223 (t80) REVERT: D 180 GLU cc_start: 0.7974 (tt0) cc_final: 0.7722 (tt0) REVERT: D 244 MET cc_start: 0.8113 (mmm) cc_final: 0.7820 (mmm) REVERT: D 302 TYR cc_start: 0.8423 (m-10) cc_final: 0.7997 (m-10) REVERT: D 338 LYS cc_start: 0.7241 (pttm) cc_final: 0.6891 (pttm) outliers start: 68 outliers final: 33 residues processed: 564 average time/residue: 0.1205 time to fit residues: 93.7082 Evaluate side-chains 570 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 532 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 194 GLN A 227 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 248 HIS C 121 GLN C 123 ASN D 30 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109197 restraints weight = 19802.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113270 restraints weight = 8997.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.115982 restraints weight = 5094.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117784 restraints weight = 3344.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119025 restraints weight = 2461.846| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12586 Z= 0.121 Angle : 0.497 8.749 17047 Z= 0.259 Chirality : 0.042 0.182 1916 Planarity : 0.004 0.062 2192 Dihedral : 4.706 57.691 1690 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.83 % Allowed : 29.54 % Favored : 64.62 % 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 aren not related in a simple way. whole: 0.36 (0.22), residues: 1520 helix: 0.92 (0.21), residues: 666 sheet: 1.78 (0.44), residues: 147 loop : -0.74 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.021 0.001 TYR A 118 PHE 0.013 0.001 PHE D 312 TRP 0.012 0.001 TRP B 201 HIS 0.005 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00275 (12586) covalent geometry : angle 0.49663 (17047) hydrogen bonds : bond 0.04112 ( 454) hydrogen bonds : angle 4.11714 ( 1302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 551 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4174 (OUTLIER) cc_final: 0.1824 (p90) REVERT: E 67 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6807 (ttm110) REVERT: E 194 ARG cc_start: 0.7205 (mtp-110) cc_final: 0.6712 (mtp-110) REVERT: E 197 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6759 (pm20) REVERT: E 241 LEU cc_start: 0.8442 (mm) cc_final: 0.8066 (mm) REVERT: E 263 TYR cc_start: 0.6940 (t80) cc_final: 0.6728 (t80) REVERT: E 300 LYS cc_start: 0.7988 (mttt) cc_final: 0.7780 (mttt) REVERT: E 316 TYR cc_start: 0.7742 (m-10) cc_final: 0.7394 (m-10) REVERT: E 322 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: E 324 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6814 (pp) REVERT: A 124 MET cc_start: 0.7697 (mmt) cc_final: 0.7397 (mmt) REVERT: A 175 ASN cc_start: 0.8062 (m-40) cc_final: 0.7788 (m-40) REVERT: A 178 LYS cc_start: 0.7952 (mtmm) cc_final: 0.7379 (mtmm) REVERT: A 329 LYS cc_start: 0.8159 (mttt) cc_final: 0.7577 (mttt) REVERT: B 157 GLU cc_start: 0.7447 (tt0) cc_final: 0.7134 (tp30) REVERT: C 43 ARG cc_start: 0.7417 (tmm160) cc_final: 0.6876 (tmm160) REVERT: C 64 GLN cc_start: 0.7992 (tp40) cc_final: 0.7639 (tp40) REVERT: C 103 TYR cc_start: 0.8488 (p90) cc_final: 0.8040 (p90) REVERT: C 199 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8450 (t) REVERT: C 215 ASN cc_start: 0.8432 (t0) cc_final: 0.8087 (t0) REVERT: C 354 THR cc_start: 0.7587 (p) cc_final: 0.7344 (p) REVERT: D 99 ILE cc_start: 0.7815 (tt) cc_final: 0.7389 (tp) REVERT: D 114 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6802 (mm-30) REVERT: D 116 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8450 (tt) REVERT: D 166 ILE cc_start: 0.6146 (OUTLIER) cc_final: 0.5843 (mp) REVERT: D 179 PHE cc_start: 0.8776 (t80) cc_final: 0.8481 (t80) REVERT: D 180 GLU cc_start: 0.7960 (tt0) cc_final: 0.7716 (tt0) REVERT: D 244 MET cc_start: 0.8121 (mmm) cc_final: 0.7759 (mmm) REVERT: D 302 TYR cc_start: 0.8425 (m-80) cc_final: 0.8005 (m-10) REVERT: D 312 PHE cc_start: 0.7082 (p90) cc_final: 0.6860 (p90) REVERT: D 338 LYS cc_start: 0.7316 (pttm) cc_final: 0.6881 (pttm) outliers start: 78 outliers final: 48 residues processed: 577 average time/residue: 0.1174 time to fit residues: 93.4816 Evaluate side-chains 602 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 546 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 42 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 HIS ** 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 = 0.3649 r_free = 0.3649 target = 0.128749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108065 restraints weight = 19768.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112149 restraints weight = 8980.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.114860 restraints weight = 5085.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116555 restraints weight = 3355.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117874 restraints weight = 2494.697| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12586 Z= 0.156 Angle : 0.533 9.263 17047 Z= 0.276 Chirality : 0.043 0.201 1916 Planarity : 0.004 0.060 2192 Dihedral : 4.482 43.672 1687 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.76 % Allowed : 30.44 % Favored : 63.80 % 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 aren not related in a simple way. whole: 0.35 (0.22), residues: 1520 helix: 0.93 (0.21), residues: 668 sheet: 1.69 (0.44), residues: 149 loop : -0.75 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 264 TYR 0.022 0.001 TYR A 118 PHE 0.014 0.001 PHE D 100 TRP 0.015 0.001 TRP B 201 HIS 0.004 0.001 HIS E 310 Details of bonding type rmsd covalent geometry : bond 0.00350 (12586) covalent geometry : angle 0.53272 (17047) hydrogen bonds : bond 0.04585 ( 454) hydrogen bonds : angle 4.20551 ( 1302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 553 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4182 (OUTLIER) cc_final: 0.1905 (p90) REVERT: E 77 ARG cc_start: 0.6351 (ttt180) cc_final: 0.6071 (ttp80) REVERT: E 194 ARG cc_start: 0.7203 (mtp-110) cc_final: 0.6715 (mtp-110) REVERT: E 197 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: E 241 LEU cc_start: 0.8451 (mm) cc_final: 0.8203 (mt) REVERT: E 300 LYS cc_start: 0.7984 (mttt) cc_final: 0.7770 (mttt) REVERT: E 308 LEU cc_start: 0.8220 (tp) cc_final: 0.7935 (tt) REVERT: E 316 TYR cc_start: 0.7738 (m-10) cc_final: 0.7386 (m-10) REVERT: E 322 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: E 324 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6839 (pp) REVERT: A 67 ASN cc_start: 0.8499 (t0) cc_final: 0.8131 (t0) REVERT: A 124 MET cc_start: 0.7713 (mmt) cc_final: 0.7405 (mmt) REVERT: A 175 ASN cc_start: 0.8061 (m-40) cc_final: 0.7831 (m-40) REVERT: A 178 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7496 (mtmm) REVERT: A 191 VAL cc_start: 0.8643 (t) cc_final: 0.8411 (p) REVERT: A 329 LYS cc_start: 0.8139 (mttt) cc_final: 0.7551 (mttt) REVERT: B 157 GLU cc_start: 0.7436 (tt0) cc_final: 0.7124 (tp30) REVERT: B 351 VAL cc_start: 0.8854 (p) cc_final: 0.8650 (t) REVERT: C 43 ARG cc_start: 0.7455 (tmm160) cc_final: 0.6935 (tmm160) REVERT: C 64 GLN cc_start: 0.8018 (tp40) cc_final: 0.7690 (tp40) REVERT: C 103 TYR cc_start: 0.8471 (p90) cc_final: 0.7960 (p90) REVERT: C 107 LEU cc_start: 0.8132 (mm) cc_final: 0.7812 (mp) REVERT: C 199 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8870 (m) REVERT: C 201 TRP cc_start: 0.7976 (OUTLIER) cc_final: 0.6698 (m-10) REVERT: C 215 ASN cc_start: 0.8458 (t0) cc_final: 0.8067 (t0) REVERT: C 287 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8306 (ttmt) REVERT: C 345 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8478 (mp) REVERT: C 354 THR cc_start: 0.7571 (p) cc_final: 0.7335 (p) REVERT: D 74 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8129 (mm) REVERT: D 114 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6813 (mm-30) REVERT: D 116 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8446 (tt) REVERT: D 166 ILE cc_start: 0.6149 (OUTLIER) cc_final: 0.5834 (mp) REVERT: D 179 PHE cc_start: 0.8758 (t80) cc_final: 0.8174 (t80) REVERT: D 244 MET cc_start: 0.8160 (mmm) cc_final: 0.7812 (mmm) REVERT: D 338 LYS cc_start: 0.7415 (pttm) cc_final: 0.6621 (pttm) outliers start: 77 outliers final: 47 residues processed: 582 average time/residue: 0.1146 time to fit residues: 92.4142 Evaluate side-chains 597 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 540 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 32 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN D 194 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109881 restraints weight = 19768.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114028 restraints weight = 9017.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116784 restraints weight = 5120.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118589 restraints weight = 3370.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119900 restraints weight = 2477.537| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12586 Z= 0.105 Angle : 0.499 9.454 17047 Z= 0.257 Chirality : 0.042 0.202 1916 Planarity : 0.004 0.059 2192 Dihedral : 4.024 34.562 1683 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.16 % Allowed : 31.71 % Favored : 63.13 % 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 aren not related in a simple way. whole: 0.37 (0.22), residues: 1520 helix: 0.91 (0.21), residues: 673 sheet: 1.85 (0.44), residues: 147 loop : -0.74 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 264 TYR 0.023 0.001 TYR A 118 PHE 0.013 0.001 PHE D 312 TRP 0.016 0.001 TRP C 201 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00242 (12586) covalent geometry : angle 0.49853 (17047) hydrogen bonds : bond 0.03527 ( 454) hydrogen bonds : angle 3.96313 ( 1302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 555 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4150 (OUTLIER) cc_final: 0.1918 (p90) REVERT: E 60 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6200 (pm20) REVERT: E 197 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: E 241 LEU cc_start: 0.8398 (mm) cc_final: 0.8036 (mm) REVERT: E 300 LYS cc_start: 0.8019 (mttt) cc_final: 0.7780 (mttt) REVERT: E 308 LEU cc_start: 0.8184 (tp) cc_final: 0.7886 (tt) REVERT: E 316 TYR cc_start: 0.7739 (m-10) cc_final: 0.7390 (m-10) REVERT: E 322 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: E 324 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6832 (pp) REVERT: A 67 ASN cc_start: 0.8418 (t0) cc_final: 0.8156 (t160) REVERT: A 124 MET cc_start: 0.7716 (mmt) cc_final: 0.7360 (mmt) REVERT: A 175 ASN cc_start: 0.8046 (m-40) cc_final: 0.7767 (m-40) REVERT: A 178 LYS cc_start: 0.8033 (mtmm) cc_final: 0.7475 (mtmm) REVERT: A 329 LYS cc_start: 0.8148 (mttt) cc_final: 0.7576 (mttt) REVERT: B 61 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7123 (mtm-85) REVERT: B 157 GLU cc_start: 0.7440 (tt0) cc_final: 0.7117 (tp30) REVERT: C 43 ARG cc_start: 0.7421 (tmm160) cc_final: 0.6899 (tmm160) REVERT: C 64 GLN cc_start: 0.8002 (tp40) cc_final: 0.7693 (tp40) REVERT: C 103 TYR cc_start: 0.8466 (p90) cc_final: 0.8043 (p90) REVERT: C 107 LEU cc_start: 0.8120 (mm) cc_final: 0.7775 (mp) REVERT: C 199 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8396 (t) REVERT: C 201 TRP cc_start: 0.7823 (OUTLIER) cc_final: 0.6524 (m-10) REVERT: C 215 ASN cc_start: 0.8479 (t0) cc_final: 0.8062 (t0) REVERT: C 287 LYS cc_start: 0.8496 (ttmt) cc_final: 0.8290 (ttmt) REVERT: C 345 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8486 (mp) REVERT: C 354 THR cc_start: 0.7471 (p) cc_final: 0.7231 (p) REVERT: D 38 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7727 (mtp180) REVERT: D 114 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6816 (mm-30) REVERT: D 116 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8376 (tt) REVERT: D 166 ILE cc_start: 0.6153 (OUTLIER) cc_final: 0.5849 (mp) REVERT: D 174 GLU cc_start: 0.8140 (tt0) cc_final: 0.7695 (tt0) REVERT: D 180 GLU cc_start: 0.8007 (tt0) cc_final: 0.7613 (tt0) REVERT: D 244 MET cc_start: 0.8152 (mmm) cc_final: 0.7863 (mmm) REVERT: D 302 TYR cc_start: 0.8399 (m-80) cc_final: 0.8016 (m-80) REVERT: D 338 LYS cc_start: 0.7347 (pttm) cc_final: 0.6858 (pttm) outliers start: 69 outliers final: 45 residues processed: 582 average time/residue: 0.1285 time to fit residues: 103.0572 Evaluate side-chains 607 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 552 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN A 194 GLN A 227 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 294 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110008 restraints weight = 19584.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.114124 restraints weight = 9013.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116812 restraints weight = 5131.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118682 restraints weight = 3409.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119971 restraints weight = 2493.689| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12586 Z= 0.102 Angle : 0.505 8.787 17047 Z= 0.259 Chirality : 0.042 0.208 1916 Planarity : 0.004 0.058 2192 Dihedral : 3.821 25.426 1680 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.64 % Allowed : 32.01 % Favored : 63.35 % 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 aren not related in a simple way. whole: 0.40 (0.22), residues: 1520 helix: 0.90 (0.21), residues: 672 sheet: 1.86 (0.44), residues: 153 loop : -0.71 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.024 0.001 TYR A 118 PHE 0.013 0.001 PHE D 312 TRP 0.017 0.001 TRP C 201 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00236 (12586) covalent geometry : angle 0.50504 (17047) hydrogen bonds : bond 0.03585 ( 454) hydrogen bonds : angle 3.92451 ( 1302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 554 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4166 (OUTLIER) cc_final: 0.1944 (p90) REVERT: E 60 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6205 (pm20) REVERT: E 197 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6623 (pm20) REVERT: E 241 LEU cc_start: 0.8385 (mm) cc_final: 0.8053 (mt) REVERT: E 300 LYS cc_start: 0.8009 (mttt) cc_final: 0.7768 (mttt) REVERT: E 308 LEU cc_start: 0.8167 (tp) cc_final: 0.7864 (tt) REVERT: E 316 TYR cc_start: 0.7745 (m-10) cc_final: 0.7387 (m-10) REVERT: E 322 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: E 324 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6834 (pp) REVERT: A 124 MET cc_start: 0.7690 (mmt) cc_final: 0.7330 (mmt) REVERT: A 175 ASN cc_start: 0.8049 (m-40) cc_final: 0.7810 (m-40) REVERT: A 178 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7527 (mtmm) REVERT: A 329 LYS cc_start: 0.8140 (mttt) cc_final: 0.7565 (mttt) REVERT: B 157 GLU cc_start: 0.7444 (tt0) cc_final: 0.7121 (tp30) REVERT: B 247 PHE cc_start: 0.8898 (m-80) cc_final: 0.8623 (m-80) REVERT: C 43 ARG cc_start: 0.7433 (tmm160) cc_final: 0.6942 (tmm160) REVERT: C 64 GLN cc_start: 0.7995 (tp40) cc_final: 0.7676 (tp40) REVERT: C 103 TYR cc_start: 0.8458 (p90) cc_final: 0.8078 (p90) REVERT: C 107 LEU cc_start: 0.8161 (mm) cc_final: 0.7835 (mp) REVERT: C 136 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6881 (tm-30) REVERT: C 199 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8407 (t) REVERT: C 201 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: C 215 ASN cc_start: 0.8484 (t0) cc_final: 0.8048 (t0) REVERT: C 287 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8284 (ttmt) REVERT: C 345 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8511 (mp) REVERT: C 354 THR cc_start: 0.7455 (p) cc_final: 0.7197 (p) REVERT: D 38 ARG cc_start: 0.7953 (mtp180) cc_final: 0.7713 (mtp180) REVERT: D 114 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6814 (mm-30) REVERT: D 116 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8377 (tt) REVERT: D 166 ILE cc_start: 0.6169 (OUTLIER) cc_final: 0.5846 (mp) REVERT: D 174 GLU cc_start: 0.8126 (tt0) cc_final: 0.7681 (tt0) REVERT: D 180 GLU cc_start: 0.7974 (tt0) cc_final: 0.7594 (tt0) REVERT: D 244 MET cc_start: 0.8187 (mmm) cc_final: 0.7811 (mmm) REVERT: D 338 LYS cc_start: 0.7370 (pttm) cc_final: 0.6729 (pttm) outliers start: 62 outliers final: 45 residues processed: 577 average time/residue: 0.1144 time to fit residues: 90.9396 Evaluate side-chains 611 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 556 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 285 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 67 optimal weight: 0.0980 chunk 147 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 141 HIS E 238 ASN A 227 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.109833 restraints weight = 19758.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113935 restraints weight = 9055.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116611 restraints weight = 5174.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118442 restraints weight = 3443.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119732 restraints weight = 2533.266| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12586 Z= 0.109 Angle : 0.504 8.418 17047 Z= 0.262 Chirality : 0.042 0.213 1916 Planarity : 0.004 0.060 2192 Dihedral : 3.811 25.820 1679 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.24 % Allowed : 31.04 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.22), residues: 1520 helix: 0.93 (0.21), residues: 666 sheet: 1.69 (0.43), residues: 159 loop : -0.71 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.025 0.001 TYR A 118 PHE 0.013 0.001 PHE D 312 TRP 0.017 0.001 TRP C 201 HIS 0.004 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00252 (12586) covalent geometry : angle 0.50381 (17047) hydrogen bonds : bond 0.03676 ( 454) hydrogen bonds : angle 3.94764 ( 1302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 563 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4156 (OUTLIER) cc_final: 0.1935 (p90) REVERT: E 60 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6199 (pm20) REVERT: E 197 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6646 (pm20) REVERT: E 227 ILE cc_start: 0.7852 (mm) cc_final: 0.7584 (mm) REVERT: E 241 LEU cc_start: 0.8440 (mm) cc_final: 0.8205 (mt) REVERT: E 300 LYS cc_start: 0.8009 (mttt) cc_final: 0.7769 (mttt) REVERT: E 308 LEU cc_start: 0.8180 (tp) cc_final: 0.7888 (tt) REVERT: E 316 TYR cc_start: 0.7735 (m-10) cc_final: 0.7422 (m-10) REVERT: E 322 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: E 324 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6845 (pp) REVERT: A 124 MET cc_start: 0.7709 (mmt) cc_final: 0.7338 (mmt) REVERT: A 175 ASN cc_start: 0.8047 (m-40) cc_final: 0.7798 (m-40) REVERT: A 178 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7538 (mtmm) REVERT: A 329 LYS cc_start: 0.8085 (mttt) cc_final: 0.7513 (mttt) REVERT: B 98 THR cc_start: 0.8504 (m) cc_final: 0.7834 (p) REVERT: B 157 GLU cc_start: 0.7435 (tt0) cc_final: 0.7109 (tp30) REVERT: B 247 PHE cc_start: 0.8898 (m-80) cc_final: 0.8622 (m-80) REVERT: C 43 ARG cc_start: 0.7447 (tmm160) cc_final: 0.6989 (tmm160) REVERT: C 64 GLN cc_start: 0.8000 (tp40) cc_final: 0.7681 (tp40) REVERT: C 103 TYR cc_start: 0.8447 (p90) cc_final: 0.8069 (p90) REVERT: C 107 LEU cc_start: 0.8179 (mm) cc_final: 0.7867 (mp) REVERT: C 136 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6881 (tm-30) REVERT: C 199 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8397 (t) REVERT: C 201 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.6515 (m-10) REVERT: C 215 ASN cc_start: 0.8505 (t0) cc_final: 0.8062 (t0) REVERT: C 252 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7776 (t0) REVERT: C 287 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8284 (ttmt) REVERT: D 38 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7718 (mtp180) REVERT: D 114 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6847 (mm-30) REVERT: D 116 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8396 (tt) REVERT: D 166 ILE cc_start: 0.6180 (OUTLIER) cc_final: 0.5858 (mp) REVERT: D 174 GLU cc_start: 0.8129 (tt0) cc_final: 0.7701 (tt0) REVERT: D 179 PHE cc_start: 0.8802 (t80) cc_final: 0.8368 (t80) REVERT: D 180 GLU cc_start: 0.8001 (tt0) cc_final: 0.7601 (tt0) REVERT: D 244 MET cc_start: 0.8217 (mmm) cc_final: 0.7847 (mmm) REVERT: D 338 LYS cc_start: 0.7359 (pttm) cc_final: 0.6879 (pttm) outliers start: 70 outliers final: 53 residues processed: 586 average time/residue: 0.1157 time to fit residues: 93.6161 Evaluate side-chains 622 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 559 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 82 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN A 227 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.109540 restraints weight = 19651.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113680 restraints weight = 9038.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116421 restraints weight = 5162.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118288 restraints weight = 3417.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119497 restraints weight = 2514.493| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12586 Z= 0.116 Angle : 0.518 8.213 17047 Z= 0.269 Chirality : 0.042 0.220 1916 Planarity : 0.004 0.059 2192 Dihedral : 3.849 26.152 1679 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.31 % Allowed : 31.19 % Favored : 63.50 % 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 aren not related in a simple way. whole: 0.43 (0.22), residues: 1520 helix: 0.99 (0.21), residues: 655 sheet: 1.65 (0.43), residues: 159 loop : -0.70 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 264 TYR 0.024 0.001 TYR A 118 PHE 0.013 0.001 PHE D 312 TRP 0.017 0.001 TRP C 201 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00268 (12586) covalent geometry : angle 0.51798 (17047) hydrogen bonds : bond 0.03761 ( 454) hydrogen bonds : angle 3.96524 ( 1302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 562 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4097 (OUTLIER) cc_final: 0.1911 (p90) REVERT: E 60 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6130 (pm20) REVERT: E 139 TYR cc_start: 0.8296 (t80) cc_final: 0.8055 (t80) REVERT: E 194 ARG cc_start: 0.7159 (mtp-110) cc_final: 0.6630 (mtp-110) REVERT: E 197 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6647 (pm20) REVERT: E 227 ILE cc_start: 0.7869 (mm) cc_final: 0.7592 (mm) REVERT: E 241 LEU cc_start: 0.8384 (mm) cc_final: 0.8011 (mm) REVERT: E 300 LYS cc_start: 0.8020 (mttt) cc_final: 0.7768 (mttt) REVERT: E 308 LEU cc_start: 0.8177 (tp) cc_final: 0.7887 (tt) REVERT: E 316 TYR cc_start: 0.7743 (m-10) cc_final: 0.7427 (m-10) REVERT: E 322 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: E 324 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6836 (pp) REVERT: A 124 MET cc_start: 0.7716 (mmt) cc_final: 0.7339 (mmt) REVERT: A 175 ASN cc_start: 0.8046 (m-40) cc_final: 0.7814 (m-40) REVERT: A 178 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7551 (mtmm) REVERT: A 213 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 329 LYS cc_start: 0.8093 (mttt) cc_final: 0.7533 (mttt) REVERT: B 61 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7136 (mtm-85) REVERT: B 98 THR cc_start: 0.8503 (m) cc_final: 0.7833 (p) REVERT: B 157 GLU cc_start: 0.7441 (tt0) cc_final: 0.7119 (tp30) REVERT: B 247 PHE cc_start: 0.8906 (m-80) cc_final: 0.8671 (m-80) REVERT: C 43 ARG cc_start: 0.7462 (tmm160) cc_final: 0.7018 (tmm160) REVERT: C 64 GLN cc_start: 0.8007 (tp40) cc_final: 0.7693 (tp40) REVERT: C 107 LEU cc_start: 0.8169 (mm) cc_final: 0.7856 (mp) REVERT: C 136 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6911 (tm-30) REVERT: C 201 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.6629 (m-10) REVERT: C 215 ASN cc_start: 0.8517 (t0) cc_final: 0.8069 (t0) REVERT: C 252 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7780 (t0) REVERT: C 256 VAL cc_start: 0.8640 (t) cc_final: 0.8308 (p) REVERT: C 287 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8293 (ttmt) REVERT: D 38 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7726 (mtp180) REVERT: D 114 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6866 (mm-30) REVERT: D 116 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8384 (tt) REVERT: D 166 ILE cc_start: 0.6169 (OUTLIER) cc_final: 0.5853 (mp) REVERT: D 174 GLU cc_start: 0.8136 (tt0) cc_final: 0.7704 (tt0) REVERT: D 179 PHE cc_start: 0.8789 (t80) cc_final: 0.8342 (t80) REVERT: D 180 GLU cc_start: 0.8013 (tt0) cc_final: 0.7606 (tt0) REVERT: D 244 MET cc_start: 0.8211 (mmm) cc_final: 0.7833 (mmm) REVERT: D 338 LYS cc_start: 0.7381 (pttm) cc_final: 0.6896 (pttm) outliers start: 71 outliers final: 53 residues processed: 585 average time/residue: 0.1296 time to fit residues: 104.3754 Evaluate side-chains 623 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 561 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 67 optimal weight: 0.0040 chunk 71 optimal weight: 2.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109365 restraints weight = 19767.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113514 restraints weight = 9056.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116297 restraints weight = 5169.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118166 restraints weight = 3409.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119453 restraints weight = 2501.319| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12586 Z= 0.122 Angle : 0.531 8.109 17047 Z= 0.277 Chirality : 0.043 0.234 1916 Planarity : 0.004 0.058 2192 Dihedral : 3.881 26.478 1679 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.01 % Allowed : 31.56 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.22), residues: 1520 helix: 1.01 (0.21), residues: 655 sheet: 1.63 (0.43), residues: 159 loop : -0.76 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 264 TYR 0.025 0.001 TYR A 118 PHE 0.013 0.001 PHE D 312 TRP 0.019 0.001 TRP C 201 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00280 (12586) covalent geometry : angle 0.53105 (17047) hydrogen bonds : bond 0.03844 ( 454) hydrogen bonds : angle 3.98211 ( 1302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 554 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4134 (OUTLIER) cc_final: 0.2006 (p90) REVERT: E 60 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6134 (pm20) REVERT: E 194 ARG cc_start: 0.7176 (mtp-110) cc_final: 0.6636 (mtp-110) REVERT: E 197 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6626 (pm20) REVERT: E 227 ILE cc_start: 0.7878 (mm) cc_final: 0.7603 (mm) REVERT: E 241 LEU cc_start: 0.8405 (mm) cc_final: 0.8016 (mm) REVERT: E 300 LYS cc_start: 0.8022 (mttt) cc_final: 0.7767 (mttt) REVERT: E 308 LEU cc_start: 0.8174 (tp) cc_final: 0.7890 (tt) REVERT: E 316 TYR cc_start: 0.7734 (m-10) cc_final: 0.7374 (m-10) REVERT: E 322 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: A 124 MET cc_start: 0.7745 (mmt) cc_final: 0.7349 (mmt) REVERT: A 175 ASN cc_start: 0.8037 (m-40) cc_final: 0.7827 (m-40) REVERT: A 178 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7564 (mtmm) REVERT: A 213 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7531 (mm-30) REVERT: A 329 LYS cc_start: 0.8060 (mttt) cc_final: 0.7502 (mttt) REVERT: B 98 THR cc_start: 0.8507 (m) cc_final: 0.7845 (p) REVERT: B 157 GLU cc_start: 0.7437 (tt0) cc_final: 0.7114 (tp30) REVERT: B 247 PHE cc_start: 0.8904 (m-80) cc_final: 0.8614 (m-80) REVERT: C 43 ARG cc_start: 0.7459 (tmm160) cc_final: 0.7021 (tmm160) REVERT: C 64 GLN cc_start: 0.8009 (tp40) cc_final: 0.7694 (tp40) REVERT: C 107 LEU cc_start: 0.8161 (mm) cc_final: 0.7845 (mp) REVERT: C 136 GLU cc_start: 0.7458 (tm-30) cc_final: 0.6918 (tm-30) REVERT: C 201 TRP cc_start: 0.7764 (OUTLIER) cc_final: 0.6692 (m-10) REVERT: C 215 ASN cc_start: 0.8523 (t0) cc_final: 0.8054 (t0) REVERT: C 252 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7782 (t0) REVERT: C 287 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8303 (ttmt) REVERT: D 38 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7729 (mtp180) REVERT: D 114 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6866 (mm-30) REVERT: D 116 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8378 (tt) REVERT: D 166 ILE cc_start: 0.6166 (OUTLIER) cc_final: 0.5847 (mp) REVERT: D 174 GLU cc_start: 0.8133 (tt0) cc_final: 0.7696 (tt0) REVERT: D 179 PHE cc_start: 0.8787 (t80) cc_final: 0.8346 (t80) REVERT: D 180 GLU cc_start: 0.8021 (tt0) cc_final: 0.7608 (tt0) REVERT: D 244 MET cc_start: 0.8208 (mmm) cc_final: 0.7863 (mmm) REVERT: D 302 TYR cc_start: 0.8389 (m-80) cc_final: 0.7964 (m-80) REVERT: D 338 LYS cc_start: 0.7410 (pttm) cc_final: 0.6912 (pttm) outliers start: 67 outliers final: 49 residues processed: 576 average time/residue: 0.1316 time to fit residues: 104.5051 Evaluate side-chains 611 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 554 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 266 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108564 restraints weight = 19578.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112674 restraints weight = 8996.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115429 restraints weight = 5136.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117267 restraints weight = 3394.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118535 restraints weight = 2500.314| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12586 Z= 0.137 Angle : 0.538 8.012 17047 Z= 0.282 Chirality : 0.043 0.233 1916 Planarity : 0.004 0.056 2192 Dihedral : 3.962 26.875 1679 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.56 % Allowed : 32.16 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.22), residues: 1520 helix: 0.97 (0.21), residues: 657 sheet: 1.47 (0.43), residues: 163 loop : -0.74 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 264 TYR 0.025 0.001 TYR A 118 PHE 0.013 0.001 PHE D 312 TRP 0.019 0.001 TRP C 201 HIS 0.004 0.001 HIS E 310 Details of bonding type rmsd covalent geometry : bond 0.00311 (12586) covalent geometry : angle 0.53835 (17047) hydrogen bonds : bond 0.04155 ( 454) hydrogen bonds : angle 4.04326 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.68 seconds wall clock time: 44 minutes 22.54 seconds (2662.54 seconds total)