Starting phenix.real_space_refine on Wed May 14 22:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvu_17972/05_2025/8pvu_17972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvu_17972/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pvu_17972/05_2025/8pvu_17972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvu_17972/05_2025/8pvu_17972.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvu_17972/05_2025/8pvu_17972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvu_17972/05_2025/8pvu_17972.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.48, per 1000 atoms: 0.61 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: 3.00 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.52 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: 3.40 Time building geometry restraints manager: 3.49 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: 1.700 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.020 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.240 ------------------------------------------------------------------------------- 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 : 7.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (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 TRP 0.040 0.002 TRP C 201 HIS 0.004 0.001 HIS E 80 PHE 0.017 0.002 PHE C 246 TYR 0.034 0.001 TYR E 193 ARG 0.008 0.000 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.25767 ( 454) hydrogen bonds : angle 6.80988 ( 1302) covalent geometry : bond 0.00468 (12586) covalent geometry : angle 0.70515 (17047) *********************** 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 : 1.254 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: 0.2809 time to fit residues: 218.0262 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 : 1.354 ------------------------------------------------------------------------------- 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 130 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 139 optimal weight: 0.1980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 GLN E 253 ASN A 67 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN C 121 GLN C 123 ASN D 37 ASN D 121 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111119 restraints weight = 19648.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115271 restraints weight = 8971.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117954 restraints weight = 5108.192| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12586 Z= 0.108 Angle : 0.506 8.784 17047 Z= 0.266 Chirality : 0.041 0.149 1916 Planarity : 0.004 0.054 2192 Dihedral : 6.472 71.229 1721 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.56 % Allowed : 27.97 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1520 helix: 0.62 (0.20), residues: 677 sheet: 1.51 (0.45), residues: 153 loop : -0.71 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.003 0.001 HIS A 84 PHE 0.016 0.001 PHE C 246 TYR 0.014 0.001 TYR E 233 ARG 0.010 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 454) hydrogen bonds : angle 4.52721 ( 1302) covalent geometry : bond 0.00240 (12586) covalent geometry : angle 0.50599 (17047) *********************** 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 617 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 556 time to evaluate : 1.255 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: 0.3875 (OUTLIER) cc_final: 0.1464 (p90) REVERT: E 60 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: E 146 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7123 (tt) REVERT: E 297 ASN cc_start: 0.8325 (t0) cc_final: 0.7281 (t0) REVERT: E 300 LYS cc_start: 0.7997 (mttt) cc_final: 0.7676 (mttt) REVERT: E 308 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7852 (tt) REVERT: E 316 TYR cc_start: 0.7786 (m-10) cc_final: 0.7512 (m-10) REVERT: E 324 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6716 (pp) REVERT: A 103 TYR cc_start: 0.8707 (p90) cc_final: 0.8465 (p90) REVERT: A 124 MET cc_start: 0.7615 (mmt) cc_final: 0.7284 (mmt) REVERT: A 175 ASN cc_start: 0.8103 (m-40) cc_final: 0.7727 (m-40) REVERT: A 178 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7414 (mtmm) REVERT: A 246 PHE cc_start: 0.8705 (t80) cc_final: 0.8440 (t80) REVERT: A 248 HIS cc_start: 0.8681 (t-90) cc_final: 0.8467 (t-170) REVERT: A 329 LYS cc_start: 0.8141 (mttt) cc_final: 0.7728 (mttt) REVERT: A 353 GLU cc_start: 0.7516 (mp0) cc_final: 0.7220 (mp0) REVERT: B 157 GLU cc_start: 0.7463 (tt0) cc_final: 0.7146 (tp30) REVERT: B 200 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8242 (mptt) REVERT: B 218 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7018 (mm-30) REVERT: B 265 LEU cc_start: 0.8516 (mt) cc_final: 0.8314 (mp) REVERT: C 43 ARG cc_start: 0.7462 (tmm160) cc_final: 0.7073 (tmm160) REVERT: C 103 TYR cc_start: 0.8405 (p90) cc_final: 0.7941 (p90) REVERT: C 206 MET cc_start: 0.7769 (ttp) cc_final: 0.7510 (ttp) REVERT: C 215 ASN cc_start: 0.8199 (t0) cc_final: 0.7957 (t0) REVERT: C 354 THR cc_start: 0.7607 (p) cc_final: 0.7373 (p) REVERT: D 99 ILE cc_start: 0.7723 (tt) cc_final: 0.7405 (tp) REVERT: D 114 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6685 (mm-30) REVERT: D 116 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8431 (tt) REVERT: D 166 ILE cc_start: 0.6075 (OUTLIER) cc_final: 0.5753 (mp) REVERT: D 179 PHE cc_start: 0.8619 (t80) cc_final: 0.8360 (t80) REVERT: D 192 MET cc_start: 0.7700 (ttm) cc_final: 0.7497 (ttm) REVERT: D 226 LYS cc_start: 0.8437 (mmmm) cc_final: 0.8046 (tppp) REVERT: D 338 LYS cc_start: 0.7242 (pttm) cc_final: 0.7019 (pttm) outliers start: 61 outliers final: 27 residues processed: 582 average time/residue: 0.2608 time to fit residues: 207.6155 Evaluate side-chains 582 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 547 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 239 HIS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 295 THR 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 195 ASN Chi-restraints excluded: chain A residue 212 LYS 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 200 LYS Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN 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 344 SER Chi-restraints excluded: chain C residue 345 LEU 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 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 285 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 135 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 227 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS C 123 ASN C 227 ASN D 30 GLN D 121 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.131037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110313 restraints weight = 19901.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114487 restraints weight = 9033.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117183 restraints weight = 5114.977| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12586 Z= 0.113 Angle : 0.495 8.972 17047 Z= 0.257 Chirality : 0.041 0.168 1916 Planarity : 0.004 0.055 2192 Dihedral : 4.731 59.245 1689 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.09 % Allowed : 28.72 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1520 helix: 0.83 (0.20), residues: 674 sheet: 1.78 (0.44), residues: 153 loop : -0.76 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS B 248 PHE 0.015 0.001 PHE B 246 TYR 0.021 0.001 TYR A 118 ARG 0.006 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 454) hydrogen bonds : angle 4.22591 ( 1302) covalent geometry : bond 0.00253 (12586) covalent geometry : angle 0.49504 (17047) *********************** 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 602 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 534 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.3971 (OUTLIER) cc_final: 0.1598 (p90) REVERT: E 60 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6476 (pm20) REVERT: E 231 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7975 (mtmm) REVERT: E 297 ASN cc_start: 0.8378 (t0) cc_final: 0.7368 (t0) REVERT: E 300 LYS cc_start: 0.7935 (mttt) cc_final: 0.7619 (mttt) REVERT: E 308 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7811 (tt) REVERT: E 316 TYR cc_start: 0.7782 (m-10) cc_final: 0.7502 (m-10) REVERT: E 324 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6733 (pp) REVERT: A 103 TYR cc_start: 0.8693 (p90) cc_final: 0.8417 (p90) REVERT: A 124 MET cc_start: 0.7651 (mmt) cc_final: 0.7344 (mmt) REVERT: A 175 ASN cc_start: 0.8064 (m-40) cc_final: 0.7758 (m-40) REVERT: A 178 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7403 (mtmm) REVERT: A 184 MET cc_start: 0.7574 (mmm) cc_final: 0.7158 (mmt) REVERT: A 248 HIS cc_start: 0.8714 (t-90) cc_final: 0.8474 (t-170) REVERT: A 329 LYS cc_start: 0.8160 (mttt) cc_final: 0.7599 (mttt) REVERT: B 157 GLU cc_start: 0.7479 (tt0) cc_final: 0.7171 (tp30) REVERT: B 200 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8263 (mptt) REVERT: C 34 TYR cc_start: 0.7828 (t80) cc_final: 0.7414 (t80) REVERT: C 43 ARG cc_start: 0.7500 (tmm160) cc_final: 0.6993 (tmm160) REVERT: C 64 GLN cc_start: 0.7992 (tp40) cc_final: 0.7669 (tp40) REVERT: C 103 TYR cc_start: 0.8480 (p90) cc_final: 0.8091 (p90) REVERT: C 190 MET cc_start: 0.8375 (tpt) cc_final: 0.7882 (tpt) REVERT: C 199 VAL cc_start: 0.8890 (p) cc_final: 0.7999 (t) REVERT: C 200 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8418 (mptt) REVERT: C 201 TRP cc_start: 0.7153 (m-10) cc_final: 0.6183 (m-10) REVERT: C 206 MET cc_start: 0.7958 (ttt) cc_final: 0.7633 (ttp) REVERT: C 215 ASN cc_start: 0.8358 (t0) cc_final: 0.7916 (t0) REVERT: C 338 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7350 (tmmt) REVERT: C 354 THR cc_start: 0.7632 (p) cc_final: 0.7394 (p) REVERT: D 38 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7763 (mtp180) REVERT: D 99 ILE cc_start: 0.7769 (tt) cc_final: 0.7376 (tp) REVERT: D 114 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6747 (mm-30) REVERT: D 116 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8460 (tt) REVERT: D 184 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7462 (mpp) REVERT: D 302 TYR cc_start: 0.8418 (m-80) cc_final: 0.7985 (m-10) REVERT: D 338 LYS cc_start: 0.7212 (pttm) cc_final: 0.6842 (pttm) outliers start: 68 outliers final: 34 residues processed: 554 average time/residue: 0.2705 time to fit residues: 204.5288 Evaluate side-chains 570 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 527 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 69 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 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 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 281 LEU 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 238 ASP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN 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 286 VAL 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 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 186 ILE 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 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 121 optimal weight: 4.9990 chunk 90 optimal weight: 0.0770 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 227 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN C 292 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106681 restraints weight = 19613.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110734 restraints weight = 8919.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.113446 restraints weight = 5083.686| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12586 Z= 0.214 Angle : 0.554 8.670 17047 Z= 0.297 Chirality : 0.045 0.190 1916 Planarity : 0.004 0.066 2192 Dihedral : 4.982 58.528 1689 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.21 % Allowed : 28.72 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1520 helix: 0.82 (0.21), residues: 670 sheet: 1.57 (0.43), residues: 155 loop : -0.76 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 201 HIS 0.004 0.001 HIS E 310 PHE 0.018 0.002 PHE D 100 TYR 0.024 0.002 TYR E 233 ARG 0.005 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.05515 ( 454) hydrogen bonds : angle 4.48979 ( 1302) covalent geometry : bond 0.00471 (12586) covalent geometry : angle 0.55424 (17047) *********************** 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 652 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 569 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4132 (OUTLIER) cc_final: 0.1879 (p90) REVERT: E 67 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6912 (ttm110) REVERT: E 194 ARG cc_start: 0.7188 (mtp-110) cc_final: 0.6680 (mtp-110) REVERT: E 197 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6803 (pm20) REVERT: E 241 LEU cc_start: 0.8487 (mm) cc_final: 0.8219 (mt) REVERT: E 263 TYR cc_start: 0.7106 (t80) cc_final: 0.6862 (t80) REVERT: E 297 ASN cc_start: 0.8473 (t0) cc_final: 0.8259 (t0) REVERT: E 308 LEU cc_start: 0.8231 (tp) cc_final: 0.7945 (tt) REVERT: E 316 TYR cc_start: 0.7720 (m-10) cc_final: 0.7378 (m-10) REVERT: E 322 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: E 324 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6792 (pp) REVERT: A 67 ASN cc_start: 0.8495 (t0) cc_final: 0.8126 (t0) REVERT: A 124 MET cc_start: 0.7772 (mmt) cc_final: 0.7476 (mmt) REVERT: A 175 ASN cc_start: 0.8134 (m-40) cc_final: 0.7777 (m-40) REVERT: A 178 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7467 (mtmm) REVERT: A 248 HIS cc_start: 0.8776 (t-90) cc_final: 0.8567 (t-170) REVERT: A 329 LYS cc_start: 0.8180 (mttt) cc_final: 0.7636 (mttt) REVERT: A 353 GLU cc_start: 0.7450 (mp0) cc_final: 0.7194 (mp0) REVERT: B 157 GLU cc_start: 0.7469 (tt0) cc_final: 0.7167 (tp30) REVERT: B 200 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8325 (mptt) REVERT: B 218 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7094 (mm-30) REVERT: B 351 VAL cc_start: 0.8945 (p) cc_final: 0.8737 (t) REVERT: C 34 TYR cc_start: 0.7846 (t80) cc_final: 0.7366 (t80) REVERT: C 43 ARG cc_start: 0.7478 (tmm160) cc_final: 0.6957 (tmm160) REVERT: C 64 GLN cc_start: 0.7993 (tp40) cc_final: 0.7617 (tp40) REVERT: C 107 LEU cc_start: 0.8124 (mm) cc_final: 0.7778 (mp) REVERT: C 215 ASN cc_start: 0.8435 (t0) cc_final: 0.8078 (t0) REVERT: C 338 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7522 (tmmt) REVERT: C 354 THR cc_start: 0.7684 (p) cc_final: 0.7448 (p) REVERT: C 359 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6766 (mmm) REVERT: D 99 ILE cc_start: 0.7930 (tt) cc_final: 0.7552 (tp) REVERT: D 114 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6827 (mm-30) REVERT: D 116 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8534 (tt) REVERT: D 166 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5775 (mp) REVERT: D 180 GLU cc_start: 0.8017 (tt0) cc_final: 0.7553 (tt0) REVERT: D 184 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7470 (mpp) REVERT: D 338 LYS cc_start: 0.7385 (pttm) cc_final: 0.6629 (pttm) outliers start: 83 outliers final: 46 residues processed: 595 average time/residue: 0.2707 time to fit residues: 219.5007 Evaluate side-chains 624 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 567 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 163 LEU 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 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 A residue 281 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 200 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 115 THR 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 204 SER Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASN 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 C residue 359 MET 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 184 MET 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 21 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 141 HIS ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN D 121 GLN ** 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 = 0.3635 r_free = 0.3635 target = 0.127856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.106921 restraints weight = 19695.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111029 restraints weight = 8976.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113736 restraints weight = 5095.399| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1819 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= 0.128 Angle : 0.508 8.321 17047 Z= 0.266 Chirality : 0.042 0.196 1916 Planarity : 0.004 0.061 2192 Dihedral : 4.392 51.579 1684 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.76 % Allowed : 30.07 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1520 helix: 0.81 (0.21), residues: 674 sheet: 1.71 (0.44), residues: 149 loop : -0.74 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 201 HIS 0.003 0.001 HIS B 248 PHE 0.012 0.001 PHE C 179 TYR 0.022 0.001 TYR A 118 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 454) hydrogen bonds : angle 4.20256 ( 1302) covalent geometry : bond 0.00289 (12586) covalent geometry : angle 0.50822 (17047) *********************** 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 645 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 568 time to evaluate : 1.400 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: 0.4090 (OUTLIER) cc_final: 0.1890 (p90) REVERT: E 60 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6268 (pm20) REVERT: E 150 LEU cc_start: 0.8749 (tt) cc_final: 0.8544 (tt) REVERT: E 194 ARG cc_start: 0.7196 (mtp-110) cc_final: 0.6709 (mtp-110) REVERT: E 197 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: E 297 ASN cc_start: 0.8451 (t0) cc_final: 0.8240 (t0) REVERT: E 316 TYR cc_start: 0.7757 (m-10) cc_final: 0.7419 (m-10) REVERT: E 324 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6860 (pp) REVERT: A 67 ASN cc_start: 0.8443 (t0) cc_final: 0.8044 (t0) REVERT: A 124 MET cc_start: 0.7708 (mmt) cc_final: 0.7393 (mmt) REVERT: A 175 ASN cc_start: 0.8064 (m-40) cc_final: 0.7787 (m-40) REVERT: A 178 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7441 (mtmm) REVERT: A 191 VAL cc_start: 0.8634 (t) cc_final: 0.8382 (p) REVERT: A 248 HIS cc_start: 0.8744 (t-90) cc_final: 0.8521 (t-170) REVERT: A 329 LYS cc_start: 0.8144 (mttt) cc_final: 0.7546 (mttt) REVERT: B 47 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 157 GLU cc_start: 0.7482 (tt0) cc_final: 0.7173 (tp30) REVERT: B 200 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8290 (mptt) REVERT: C 34 TYR cc_start: 0.7745 (t80) cc_final: 0.7289 (t80) REVERT: C 43 ARG cc_start: 0.7462 (tmm160) cc_final: 0.6939 (tmm160) REVERT: C 64 GLN cc_start: 0.8009 (tp40) cc_final: 0.7670 (tp40) REVERT: C 103 TYR cc_start: 0.8494 (p90) cc_final: 0.7992 (p90) REVERT: C 199 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8819 (m) REVERT: C 201 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.6568 (m-10) REVERT: C 215 ASN cc_start: 0.8453 (t0) cc_final: 0.8056 (t0) REVERT: C 345 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8478 (mp) REVERT: C 354 THR cc_start: 0.7623 (p) cc_final: 0.7397 (p) REVERT: D 74 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8153 (mm) REVERT: D 114 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6804 (mm-30) REVERT: D 116 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8443 (tt) REVERT: D 166 ILE cc_start: 0.6081 (OUTLIER) cc_final: 0.5783 (mp) REVERT: D 180 GLU cc_start: 0.8006 (tt0) cc_final: 0.7784 (tt0) REVERT: D 213 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: D 338 LYS cc_start: 0.7394 (pttm) cc_final: 0.6769 (pttm) outliers start: 77 outliers final: 44 residues processed: 598 average time/residue: 0.2623 time to fit residues: 214.2848 Evaluate side-chains 605 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 549 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 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 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 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 344 SER 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 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 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 171 VAL 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 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 213 GLU 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 6 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 143 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 294 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108114 restraints weight = 19982.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112257 restraints weight = 9043.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115029 restraints weight = 5119.264| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1924 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= 0.140 Angle : 0.521 9.266 17047 Z= 0.271 Chirality : 0.043 0.207 1916 Planarity : 0.004 0.060 2192 Dihedral : 4.163 45.507 1680 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.53 % Allowed : 30.37 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1520 helix: 0.89 (0.21), residues: 670 sheet: 1.74 (0.44), residues: 149 loop : -0.75 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 201 HIS 0.003 0.001 HIS E 310 PHE 0.012 0.001 PHE C 179 TYR 0.023 0.001 TYR A 118 ARG 0.006 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 454) hydrogen bonds : angle 4.18482 ( 1302) covalent geometry : bond 0.00314 (12586) covalent geometry : angle 0.52121 (17047) *********************** 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 637 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 563 time to evaluate : 1.373 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: 0.4106 (OUTLIER) cc_final: 0.1960 (p90) REVERT: E 60 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6273 (pm20) REVERT: E 194 ARG cc_start: 0.7206 (mtp-110) cc_final: 0.6706 (mtp-110) REVERT: E 197 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6797 (pm20) REVERT: E 241 LEU cc_start: 0.8482 (mm) cc_final: 0.8174 (mt) REVERT: E 297 ASN cc_start: 0.8467 (t0) cc_final: 0.8252 (t0) REVERT: E 308 LEU cc_start: 0.8263 (tp) cc_final: 0.7936 (tt) REVERT: E 316 TYR cc_start: 0.7758 (m-10) cc_final: 0.7418 (m-10) REVERT: E 322 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: E 324 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6853 (pp) REVERT: A 67 ASN cc_start: 0.8469 (t0) cc_final: 0.8087 (t0) REVERT: A 124 MET cc_start: 0.7792 (mmt) cc_final: 0.7442 (mmt) REVERT: A 175 ASN cc_start: 0.8071 (m-40) cc_final: 0.7825 (m-40) REVERT: A 178 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7480 (mtmm) REVERT: A 191 VAL cc_start: 0.8624 (t) cc_final: 0.8372 (p) REVERT: A 248 HIS cc_start: 0.8757 (t-90) cc_final: 0.8539 (t-170) REVERT: A 329 LYS cc_start: 0.8153 (mttt) cc_final: 0.7587 (mttt) REVERT: B 47 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 157 GLU cc_start: 0.7475 (tt0) cc_final: 0.7159 (tp30) REVERT: B 200 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8304 (mptt) REVERT: B 201 TRP cc_start: 0.8171 (m100) cc_final: 0.7536 (m-10) REVERT: B 218 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7085 (mm-30) REVERT: C 43 ARG cc_start: 0.7470 (tmm160) cc_final: 0.6996 (tmm160) REVERT: C 64 GLN cc_start: 0.8021 (tp40) cc_final: 0.7681 (tp40) REVERT: C 103 TYR cc_start: 0.8505 (p90) cc_final: 0.8046 (p90) REVERT: C 107 LEU cc_start: 0.8143 (mm) cc_final: 0.7818 (mp) REVERT: C 199 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8850 (m) REVERT: C 201 TRP cc_start: 0.7897 (OUTLIER) cc_final: 0.6730 (m-10) REVERT: C 215 ASN cc_start: 0.8464 (t0) cc_final: 0.8044 (t0) REVERT: C 256 VAL cc_start: 0.8575 (t) cc_final: 0.8358 (p) REVERT: C 345 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8491 (mp) REVERT: C 354 THR cc_start: 0.7606 (p) cc_final: 0.7380 (p) REVERT: D 114 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6829 (mm-30) REVERT: D 116 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8439 (tt) REVERT: D 166 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5799 (mp) REVERT: D 180 GLU cc_start: 0.7955 (tt0) cc_final: 0.7637 (tt0) REVERT: D 213 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: D 338 LYS cc_start: 0.7428 (pttm) cc_final: 0.6892 (pttm) outliers start: 74 outliers final: 45 residues processed: 595 average time/residue: 0.2675 time to fit residues: 220.0495 Evaluate side-chains 620 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 563 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 75 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 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 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 255 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 LEU 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 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 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU 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 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 186 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 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 8 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 114 optimal weight: 0.0980 chunk 72 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 292 ASN D 194 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106003 restraints weight = 19935.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110118 restraints weight = 9023.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.112884 restraints weight = 5127.690| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12586 Z= 0.144 Angle : 0.523 6.497 17047 Z= 0.273 Chirality : 0.043 0.218 1916 Planarity : 0.004 0.060 2192 Dihedral : 4.121 34.920 1680 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.68 % Allowed : 30.44 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1520 helix: 0.89 (0.21), residues: 669 sheet: 1.52 (0.43), residues: 157 loop : -0.78 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 201 HIS 0.004 0.001 HIS B 248 PHE 0.013 0.001 PHE D 100 TYR 0.021 0.001 TYR A 118 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 454) hydrogen bonds : angle 4.17104 ( 1302) covalent geometry : bond 0.00324 (12586) covalent geometry : angle 0.52271 (17047) *********************** 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 631 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 555 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4085 (OUTLIER) cc_final: 0.2060 (p90) REVERT: E 60 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6285 (pm20) REVERT: E 150 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8569 (tt) REVERT: E 194 ARG cc_start: 0.7225 (mtp-110) cc_final: 0.6698 (mtp-110) REVERT: E 197 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6774 (pm20) REVERT: E 241 LEU cc_start: 0.8477 (mm) cc_final: 0.8217 (mt) REVERT: E 297 ASN cc_start: 0.8469 (t0) cc_final: 0.8235 (t0) REVERT: E 308 LEU cc_start: 0.8226 (tp) cc_final: 0.7908 (tt) REVERT: E 316 TYR cc_start: 0.7762 (m-10) cc_final: 0.7443 (m-10) REVERT: E 322 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: E 324 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6844 (pp) REVERT: A 178 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7535 (mtmm) REVERT: A 191 VAL cc_start: 0.8605 (t) cc_final: 0.8359 (p) REVERT: A 213 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7588 (mm-30) REVERT: A 248 HIS cc_start: 0.8760 (t-90) cc_final: 0.8540 (t-170) REVERT: A 329 LYS cc_start: 0.8115 (mttt) cc_final: 0.7536 (mttt) REVERT: B 47 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7862 (tm-30) REVERT: B 157 GLU cc_start: 0.7479 (tt0) cc_final: 0.7160 (tp30) REVERT: B 200 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8301 (mptt) REVERT: C 43 ARG cc_start: 0.7504 (tmm160) cc_final: 0.7018 (tmm160) REVERT: C 64 GLN cc_start: 0.8027 (tp40) cc_final: 0.7676 (tp40) REVERT: C 103 TYR cc_start: 0.8488 (p90) cc_final: 0.7951 (p90) REVERT: C 107 LEU cc_start: 0.8120 (mm) cc_final: 0.7808 (mp) REVERT: C 136 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6929 (tm-30) REVERT: C 201 TRP cc_start: 0.7873 (OUTLIER) cc_final: 0.6833 (m-10) REVERT: C 215 ASN cc_start: 0.8470 (t0) cc_final: 0.8042 (t0) REVERT: C 256 VAL cc_start: 0.8625 (t) cc_final: 0.8379 (p) REVERT: C 345 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8489 (mp) REVERT: C 354 THR cc_start: 0.7580 (p) cc_final: 0.7365 (p) REVERT: D 114 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6838 (mm-30) REVERT: D 116 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8422 (tt) REVERT: D 166 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.5775 (mp) REVERT: D 174 GLU cc_start: 0.8228 (tt0) cc_final: 0.7755 (tt0) REVERT: D 180 GLU cc_start: 0.7949 (tt0) cc_final: 0.7593 (tt0) REVERT: D 213 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: D 338 LYS cc_start: 0.7484 (pttm) cc_final: 0.6914 (pttm) outliers start: 76 outliers final: 54 residues processed: 583 average time/residue: 0.2632 time to fit residues: 209.4585 Evaluate side-chains 620 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 554 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 138 LYS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 163 LEU 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 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 255 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 344 SER 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 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 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 296 MET Chi-restraints excluded: chain C residue 69 MET 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 201 TRP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASN 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 187 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 142 optimal weight: 0.0060 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.9596 ------------------------------------------------------------------------------- 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 123 ASN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107669 restraints weight = 19893.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111835 restraints weight = 8996.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114615 restraints weight = 5079.729| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2062 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= 0.139 Angle : 0.528 8.834 17047 Z= 0.275 Chirality : 0.043 0.230 1916 Planarity : 0.004 0.061 2192 Dihedral : 4.075 24.751 1680 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.61 % Allowed : 30.52 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1520 helix: 0.90 (0.21), residues: 659 sheet: 1.76 (0.44), residues: 149 loop : -0.77 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 201 HIS 0.004 0.001 HIS B 248 PHE 0.012 0.001 PHE D 312 TYR 0.022 0.001 TYR A 118 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 454) hydrogen bonds : angle 4.14979 ( 1302) covalent geometry : bond 0.00315 (12586) covalent geometry : angle 0.52826 (17047) *********************** 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 628 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 553 time to evaluate : 1.287 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: 0.4068 (OUTLIER) cc_final: 0.2079 (p90) REVERT: E 60 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6279 (pm20) REVERT: E 150 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8587 (tt) REVERT: E 194 ARG cc_start: 0.7225 (mtp-110) cc_final: 0.6703 (mtp-110) REVERT: E 297 ASN cc_start: 0.8475 (t0) cc_final: 0.8237 (t0) REVERT: E 308 LEU cc_start: 0.8236 (tp) cc_final: 0.7942 (tt) REVERT: E 316 TYR cc_start: 0.7768 (m-10) cc_final: 0.7445 (m-10) REVERT: E 322 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: E 324 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6862 (pp) REVERT: A 67 ASN cc_start: 0.8456 (t0) cc_final: 0.8066 (t0) REVERT: A 124 MET cc_start: 0.7841 (mmt) cc_final: 0.7436 (mmt) REVERT: A 178 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7545 (mtmm) REVERT: A 191 VAL cc_start: 0.8601 (t) cc_final: 0.8358 (p) REVERT: A 213 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7581 (mm-30) REVERT: A 248 HIS cc_start: 0.8754 (t-90) cc_final: 0.8536 (t-170) REVERT: A 329 LYS cc_start: 0.8105 (mttt) cc_final: 0.7522 (mttt) REVERT: B 47 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 157 GLU cc_start: 0.7475 (tt0) cc_final: 0.7162 (tp30) REVERT: B 200 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8295 (mptt) REVERT: C 43 ARG cc_start: 0.7485 (tmm160) cc_final: 0.7042 (tmm160) REVERT: C 64 GLN cc_start: 0.8024 (tp40) cc_final: 0.7707 (tp40) REVERT: C 103 TYR cc_start: 0.8479 (p90) cc_final: 0.7924 (p90) REVERT: C 107 LEU cc_start: 0.8120 (mm) cc_final: 0.7804 (mp) REVERT: C 136 GLU cc_start: 0.7475 (tm-30) cc_final: 0.6935 (tm-30) REVERT: C 201 TRP cc_start: 0.7811 (OUTLIER) cc_final: 0.6822 (m-10) REVERT: C 215 ASN cc_start: 0.8472 (t0) cc_final: 0.8032 (t0) REVERT: C 256 VAL cc_start: 0.8609 (t) cc_final: 0.8355 (p) REVERT: C 345 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8501 (mp) REVERT: C 354 THR cc_start: 0.7579 (p) cc_final: 0.7361 (p) REVERT: D 114 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6831 (mm-30) REVERT: D 116 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8414 (tt) REVERT: D 166 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5785 (mp) REVERT: D 174 GLU cc_start: 0.8219 (tt0) cc_final: 0.7753 (tt0) REVERT: D 180 GLU cc_start: 0.7945 (tt0) cc_final: 0.7576 (tt0) REVERT: D 213 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: D 302 TYR cc_start: 0.8459 (m-80) cc_final: 0.8004 (m-80) REVERT: D 338 LYS cc_start: 0.7498 (pttm) cc_final: 0.6925 (pttm) outliers start: 75 outliers final: 56 residues processed: 582 average time/residue: 0.2655 time to fit residues: 211.2415 Evaluate side-chains 615 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 548 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 115 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 163 LEU 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 269 HIS Chi-restraints excluded: chain E residue 292 LYS 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 255 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 344 SER 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 200 LYS 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 296 MET Chi-restraints excluded: chain C residue 69 MET 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 201 TRP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 286 VAL 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 106 ASN 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 187 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 72 optimal weight: 0.2980 chunk 93 optimal weight: 0.0870 chunk 115 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 73 optimal weight: 0.0470 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 145 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 292 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110935 restraints weight = 19880.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115190 restraints weight = 9091.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117999 restraints weight = 5170.562| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12586 Z= 0.090 Angle : 0.501 6.713 17047 Z= 0.257 Chirality : 0.041 0.217 1916 Planarity : 0.004 0.059 2192 Dihedral : 3.764 25.162 1679 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.19 % Allowed : 31.94 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1520 helix: 0.84 (0.21), residues: 679 sheet: 1.69 (0.44), residues: 159 loop : -0.74 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 201 HIS 0.003 0.000 HIS B 248 PHE 0.012 0.001 PHE D 312 TYR 0.025 0.001 TYR A 118 ARG 0.006 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 454) hydrogen bonds : angle 3.91294 ( 1302) covalent geometry : bond 0.00206 (12586) covalent geometry : angle 0.50057 (17047) *********************** 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 600 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 544 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4021 (OUTLIER) cc_final: 0.1988 (p90) REVERT: E 60 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6141 (pm20) REVERT: E 227 ILE cc_start: 0.7744 (mm) cc_final: 0.7476 (mm) REVERT: E 308 LEU cc_start: 0.8222 (tp) cc_final: 0.8009 (tp) REVERT: E 316 TYR cc_start: 0.7756 (m-10) cc_final: 0.7435 (m-10) REVERT: A 46 LEU cc_start: 0.8555 (mt) cc_final: 0.8305 (mp) REVERT: A 67 ASN cc_start: 0.8385 (t0) cc_final: 0.8118 (t160) REVERT: A 124 MET cc_start: 0.7718 (mmt) cc_final: 0.7322 (mmt) REVERT: A 178 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7538 (mtmm) REVERT: A 184 MET cc_start: 0.7572 (mmm) cc_final: 0.7284 (mmt) REVERT: A 213 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 281 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 329 LYS cc_start: 0.8073 (mttt) cc_final: 0.7473 (mttt) REVERT: B 47 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 157 GLU cc_start: 0.7487 (tt0) cc_final: 0.7156 (tp30) REVERT: B 200 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8193 (mptt) REVERT: B 247 PHE cc_start: 0.8880 (m-80) cc_final: 0.8603 (m-80) REVERT: C 43 ARG cc_start: 0.7396 (tmm160) cc_final: 0.6978 (tmm160) REVERT: C 103 TYR cc_start: 0.8416 (p90) cc_final: 0.8019 (p90) REVERT: C 107 LEU cc_start: 0.8131 (mm) cc_final: 0.7813 (mp) REVERT: C 136 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6908 (tm-30) REVERT: C 190 MET cc_start: 0.8597 (tpp) cc_final: 0.7497 (tpt) REVERT: C 201 TRP cc_start: 0.7544 (OUTLIER) cc_final: 0.6213 (m-10) REVERT: C 215 ASN cc_start: 0.8464 (t0) cc_final: 0.8004 (t0) REVERT: C 256 VAL cc_start: 0.8603 (t) cc_final: 0.8365 (p) REVERT: C 354 THR cc_start: 0.7536 (p) cc_final: 0.7285 (p) REVERT: D 38 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7708 (mtp180) REVERT: D 109 SER cc_start: 0.7651 (p) cc_final: 0.7268 (t) REVERT: D 114 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6813 (mm-30) REVERT: D 137 GLU cc_start: 0.7697 (tp30) cc_final: 0.7174 (tt0) REVERT: D 166 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5793 (mp) REVERT: D 174 GLU cc_start: 0.8190 (tt0) cc_final: 0.7742 (tt0) REVERT: D 180 GLU cc_start: 0.7915 (tt0) cc_final: 0.7529 (tt0) REVERT: D 213 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: D 302 TYR cc_start: 0.8375 (m-80) cc_final: 0.8046 (m-80) REVERT: D 338 LYS cc_start: 0.7402 (pttm) cc_final: 0.6933 (pttm) outliers start: 56 outliers final: 35 residues processed: 566 average time/residue: 0.2582 time to fit residues: 201.6158 Evaluate side-chains 583 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 541 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 239 HIS 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 218 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 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 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 69 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 286 VAL Chi-restraints excluded: chain C residue 292 ASN 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 166 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE 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 8 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 98 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 227 ASN ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 292 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108755 restraints weight = 19590.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112944 restraints weight = 9011.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115693 restraints weight = 5144.682| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12586 Z= 0.138 Angle : 0.543 11.728 17047 Z= 0.280 Chirality : 0.043 0.233 1916 Planarity : 0.004 0.059 2192 Dihedral : 3.897 27.139 1679 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.52 % Allowed : 33.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1520 helix: 0.91 (0.21), residues: 660 sheet: 1.62 (0.43), residues: 159 loop : -0.75 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 201 HIS 0.005 0.001 HIS A 248 PHE 0.015 0.001 PHE C 355 TYR 0.025 0.001 TYR A 118 ARG 0.005 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 454) hydrogen bonds : angle 4.04039 ( 1302) covalent geometry : bond 0.00315 (12586) covalent geometry : angle 0.54300 (17047) ********************** 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 604 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 557 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4091 (OUTLIER) cc_final: 0.2069 (p90) REVERT: E 60 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6183 (pm20) REVERT: E 151 LYS cc_start: 0.8427 (pttt) cc_final: 0.7970 (pttt) REVERT: E 227 ILE cc_start: 0.7882 (mm) cc_final: 0.7615 (mm) REVERT: E 241 LEU cc_start: 0.8455 (mm) cc_final: 0.8133 (mt) REVERT: E 308 LEU cc_start: 0.8252 (tp) cc_final: 0.7932 (tt) REVERT: E 316 TYR cc_start: 0.7763 (m-10) cc_final: 0.7428 (m-10) REVERT: A 46 LEU cc_start: 0.8575 (mt) cc_final: 0.8311 (mp) REVERT: A 67 ASN cc_start: 0.8476 (t0) cc_final: 0.8127 (t0) REVERT: A 124 MET cc_start: 0.7797 (mmt) cc_final: 0.7369 (mmt) REVERT: A 178 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7614 (mtmm) REVERT: A 184 MET cc_start: 0.7690 (mmm) cc_final: 0.7397 (mmt) REVERT: A 191 VAL cc_start: 0.8585 (t) cc_final: 0.8341 (p) REVERT: A 213 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7733 (mm-30) REVERT: A 329 LYS cc_start: 0.8052 (mttt) cc_final: 0.7500 (mttt) REVERT: B 47 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 157 GLU cc_start: 0.7489 (tt0) cc_final: 0.7171 (tp30) REVERT: B 200 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8294 (mptt) REVERT: B 218 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7062 (mm-30) REVERT: B 247 PHE cc_start: 0.8905 (m-80) cc_final: 0.8567 (m-80) REVERT: C 43 ARG cc_start: 0.7460 (tmm160) cc_final: 0.7011 (tmm160) REVERT: C 64 GLN cc_start: 0.8024 (tp40) cc_final: 0.7684 (tp40) REVERT: C 107 LEU cc_start: 0.8171 (mm) cc_final: 0.7847 (mp) REVERT: C 136 GLU cc_start: 0.7469 (tm-30) cc_final: 0.6939 (tm-30) REVERT: C 190 MET cc_start: 0.8666 (tpp) cc_final: 0.7595 (tpt) REVERT: C 201 TRP cc_start: 0.7712 (OUTLIER) cc_final: 0.6569 (m-10) REVERT: C 215 ASN cc_start: 0.8494 (t0) cc_final: 0.8020 (t0) REVERT: C 256 VAL cc_start: 0.8608 (t) cc_final: 0.8359 (p) REVERT: C 354 THR cc_start: 0.7432 (p) cc_final: 0.7195 (p) REVERT: D 64 GLN cc_start: 0.7688 (tt0) cc_final: 0.7473 (tp40) REVERT: D 109 SER cc_start: 0.7626 (p) cc_final: 0.7207 (t) REVERT: D 114 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6844 (mm-30) REVERT: D 137 GLU cc_start: 0.7715 (tp30) cc_final: 0.7206 (tt0) REVERT: D 166 ILE cc_start: 0.6124 (OUTLIER) cc_final: 0.5799 (mp) REVERT: D 174 GLU cc_start: 0.8193 (tt0) cc_final: 0.7744 (tt0) REVERT: D 180 GLU cc_start: 0.7916 (tt0) cc_final: 0.7538 (tt0) REVERT: D 209 ARG cc_start: 0.8554 (tpt-90) cc_final: 0.8308 (tpt-90) REVERT: D 213 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: D 338 LYS cc_start: 0.7453 (pttm) cc_final: 0.6908 (pttm) outliers start: 47 outliers final: 37 residues processed: 575 average time/residue: 0.2687 time to fit residues: 211.1565 Evaluate side-chains 598 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 555 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 236 GLN Chi-restraints excluded: chain E residue 239 HIS 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 218 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 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 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 238 ASP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 296 MET 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 201 TRP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASN 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 166 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 344 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 292 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108661 restraints weight = 19688.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112877 restraints weight = 9058.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115645 restraints weight = 5158.858| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2263 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= 0.117 Angle : 0.535 10.785 17047 Z= 0.275 Chirality : 0.042 0.225 1916 Planarity : 0.004 0.057 2192 Dihedral : 3.888 27.550 1679 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.59 % Allowed : 32.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1520 helix: 0.93 (0.21), residues: 664 sheet: 1.62 (0.43), residues: 159 loop : -0.75 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 201 HIS 0.003 0.001 HIS B 248 PHE 0.012 0.001 PHE D 312 TYR 0.025 0.001 TYR A 118 ARG 0.005 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 454) hydrogen bonds : angle 4.00041 ( 1302) covalent geometry : bond 0.00271 (12586) covalent geometry : angle 0.53494 (17047) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4969.77 seconds wall clock time: 87 minutes 6.96 seconds (5226.96 seconds total)