Starting phenix.real_space_refine on Wed Jul 30 12:07:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvu_17972/07_2025/8pvu_17972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvu_17972/07_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_17972/07_2025/8pvu_17972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvu_17972/07_2025/8pvu_17972.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvu_17972/07_2025/8pvu_17972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvu_17972/07_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-5711/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: 7.45, per 1000 atoms: 0.60 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: 2.95 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: 1.44 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: 3.36 Time building geometry restraints manager: 3.51 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: 1.300 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.160 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.520 ------------------------------------------------------------------------------- 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 : 1.189 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: 0.2729 time to fit residues: 212.4514 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 : 1.210 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111119 restraints weight = 19648.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115272 restraints weight = 8971.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117956 restraints weight = 5108.043| |-----------------------------------------------------------------------------| 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 : 1.390 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: 0.3878 (OUTLIER) cc_final: 0.1465 (p90) REVERT: E 60 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6557 (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: 0.6999 (OUTLIER) cc_final: 0.6717 (pp) REVERT: A 103 TYR cc_start: 0.8707 (p90) cc_final: 0.8466 (p90) REVERT: A 124 MET cc_start: 0.7616 (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: 0.8682 (t-90) cc_final: 0.8467 (t-170) REVERT: A 329 LYS cc_start: 0.8140 (mttt) cc_final: 0.7727 (mttt) REVERT: A 353 GLU cc_start: 0.7517 (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: 0.7938 (p90) REVERT: C 206 MET cc_start: 0.7769 (ttp) cc_final: 0.7511 (ttp) REVERT: C 215 ASN cc_start: 0.8198 (t0) cc_final: 0.7956 (t0) REVERT: C 354 THR cc_start: 0.7607 (p) cc_final: 0.7373 (p) REVERT: D 99 ILE cc_start: 0.7724 (tt) cc_final: 0.7405 (tp) REVERT: D 114 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6686 (mm-30) REVERT: D 116 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8430 (tt) REVERT: D 166 ILE cc_start: 0.6074 (OUTLIER) cc_final: 0.5752 (mp) REVERT: D 179 PHE cc_start: 0.8619 (t80) cc_final: 0.8361 (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: 0.7020 (pttm) outliers start: 61 outliers final: 27 residues processed: 582 average time/residue: 0.2692 time to fit residues: 214.9560 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 : 1.336 ------------------------------------------------------------------------------- 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: 3.9990 chunk 9 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 C 292 ASN D 30 GLN D 121 GLN ** D 248 HIS ** 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 = 0.3672 r_free = 0.3672 target = 0.130473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109780 restraints weight = 19921.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113932 restraints weight = 9023.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116670 restraints weight = 5096.871| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1545 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= 0.124 Angle : 0.502 9.012 17047 Z= 0.262 Chirality : 0.042 0.169 1916 Planarity : 0.004 0.055 2192 Dihedral : 4.794 59.290 1689 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.31 % Allowed : 28.72 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1520 helix: 0.83 (0.20), residues: 671 sheet: 1.74 (0.44), residues: 153 loop : -0.75 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 201 HIS 0.006 0.001 HIS B 248 PHE 0.015 0.001 PHE B 246 TYR 0.020 0.001 TYR A 118 ARG 0.006 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 454) hydrogen bonds : angle 4.28450 ( 1302) covalent geometry : bond 0.00280 (12586) covalent geometry : angle 0.50247 (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 612 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 541 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.3980 (OUTLIER) cc_final: 0.1607 (p90) REVERT: E 60 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: E 231 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7960 (mtmm) REVERT: E 297 ASN cc_start: 0.8384 (t0) cc_final: 0.7371 (t0) REVERT: E 300 LYS cc_start: 0.7951 (mttt) cc_final: 0.7627 (mttt) REVERT: E 308 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7810 (tt) REVERT: E 316 TYR cc_start: 0.7782 (m-10) cc_final: 0.7498 (m-10) REVERT: E 324 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6731 (pp) REVERT: A 103 TYR cc_start: 0.8699 (p90) cc_final: 0.8466 (p90) REVERT: A 124 MET cc_start: 0.7672 (mmt) cc_final: 0.7349 (mmt) REVERT: A 175 ASN cc_start: 0.8087 (m-40) cc_final: 0.7754 (m-40) REVERT: A 178 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7395 (mtmm) REVERT: A 184 MET cc_start: 0.7610 (mmm) cc_final: 0.7186 (mmt) REVERT: A 248 HIS cc_start: 0.8730 (t-90) cc_final: 0.8483 (t-170) REVERT: A 329 LYS cc_start: 0.8163 (mttt) cc_final: 0.7606 (mttt) REVERT: B 157 GLU cc_start: 0.7476 (tt0) cc_final: 0.7173 (tp30) REVERT: B 200 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8277 (mptt) REVERT: C 34 TYR cc_start: 0.7831 (t80) cc_final: 0.7412 (t80) REVERT: C 43 ARG cc_start: 0.7509 (tmm160) cc_final: 0.7005 (tmm160) REVERT: C 64 GLN cc_start: 0.7995 (tp40) cc_final: 0.7644 (tp40) REVERT: C 103 TYR cc_start: 0.8485 (p90) cc_final: 0.8049 (p90) REVERT: C 190 MET cc_start: 0.8396 (tpt) cc_final: 0.7882 (tpt) REVERT: C 201 TRP cc_start: 0.7192 (m-10) cc_final: 0.6346 (m-10) REVERT: C 206 MET cc_start: 0.7944 (ttt) cc_final: 0.7619 (ttp) REVERT: C 215 ASN cc_start: 0.8355 (t0) cc_final: 0.7915 (t0) REVERT: C 338 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7346 (tmmt) REVERT: C 354 THR cc_start: 0.7641 (p) cc_final: 0.7401 (p) REVERT: D 38 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7773 (mtp180) REVERT: D 99 ILE cc_start: 0.7822 (tt) cc_final: 0.7429 (tp) REVERT: D 114 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6750 (mm-30) REVERT: D 116 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8487 (tt) REVERT: D 184 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7475 (mpp) REVERT: D 338 LYS cc_start: 0.7231 (pttm) cc_final: 0.6861 (pttm) outliers start: 71 outliers final: 38 residues processed: 562 average time/residue: 0.2707 time to fit residues: 207.4381 Evaluate side-chains 580 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 534 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 236 GLN 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 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 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 202 THR 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 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 70 ILE 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: 6.9990 chunk 90 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- 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 D 121 GLN ** 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 = 0.3629 r_free = 0.3629 target = 0.127347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106583 restraints weight = 19605.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110665 restraints weight = 8910.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113370 restraints weight = 5063.799| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1673 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= 0.215 Angle : 0.560 8.959 17047 Z= 0.300 Chirality : 0.045 0.191 1916 Planarity : 0.004 0.064 2192 Dihedral : 5.001 58.089 1689 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.83 % Allowed : 28.80 % Favored : 65.37 % 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: 0.24 (0.22), residues: 1520 helix: 0.80 (0.21), residues: 669 sheet: 1.55 (0.43), residues: 155 loop : -0.77 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 201 HIS 0.004 0.001 HIS D 122 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 0.05588 ( 454) hydrogen bonds : angle 4.51233 ( 1302) covalent geometry : bond 0.00472 (12586) covalent geometry : angle 0.56025 (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 645 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 567 time to evaluate : 1.416 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: 0.4151 (OUTLIER) cc_final: 0.1916 (p90) REVERT: E 194 ARG cc_start: 0.7179 (mtp-110) cc_final: 0.6710 (mtp-110) REVERT: E 197 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6803 (pm20) REVERT: E 241 LEU cc_start: 0.8491 (mm) cc_final: 0.8213 (mt) REVERT: E 297 ASN cc_start: 0.8470 (t0) cc_final: 0.8249 (t0) REVERT: E 308 LEU cc_start: 0.8229 (tp) cc_final: 0.7895 (tt) REVERT: E 316 TYR cc_start: 0.7744 (m-10) cc_final: 0.7395 (m-10) REVERT: E 324 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6804 (pp) REVERT: A 67 ASN cc_start: 0.8499 (t0) cc_final: 0.8130 (t0) REVERT: A 124 MET cc_start: 0.7785 (mmt) cc_final: 0.7378 (mmt) REVERT: A 175 ASN cc_start: 0.8130 (m-40) cc_final: 0.7763 (m-40) REVERT: A 178 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7457 (mtmm) REVERT: A 248 HIS cc_start: 0.8777 (t-90) cc_final: 0.8571 (t-170) REVERT: A 329 LYS cc_start: 0.8180 (mttt) cc_final: 0.7634 (mttt) REVERT: A 353 GLU cc_start: 0.7420 (mp0) cc_final: 0.7175 (mp0) REVERT: B 157 GLU cc_start: 0.7464 (tt0) cc_final: 0.7167 (tp30) REVERT: B 200 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8313 (mptt) REVERT: B 218 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 264 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7473 (mtp85) REVERT: B 351 VAL cc_start: 0.8946 (p) cc_final: 0.8733 (t) REVERT: C 34 TYR cc_start: 0.7838 (t80) cc_final: 0.7347 (t80) REVERT: C 43 ARG cc_start: 0.7475 (tmm160) cc_final: 0.6959 (tmm160) REVERT: C 64 GLN cc_start: 0.7993 (tp40) cc_final: 0.7618 (tp40) REVERT: C 107 LEU cc_start: 0.8124 (mm) cc_final: 0.7776 (mp) REVERT: C 213 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6580 (tm-30) REVERT: C 215 ASN cc_start: 0.8431 (t0) cc_final: 0.8078 (t0) REVERT: C 338 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7530 (tmmt) REVERT: C 354 THR cc_start: 0.7687 (p) cc_final: 0.7451 (p) REVERT: C 359 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6763 (mmm) REVERT: D 99 ILE cc_start: 0.7929 (tt) cc_final: 0.7562 (tp) REVERT: D 114 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6831 (mm-30) REVERT: D 116 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8546 (tt) REVERT: D 166 ILE cc_start: 0.6064 (OUTLIER) cc_final: 0.5771 (mp) REVERT: D 180 GLU cc_start: 0.8014 (tt0) cc_final: 0.7553 (tt0) REVERT: D 184 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7463 (mpp) REVERT: D 226 LYS cc_start: 0.8466 (mmmm) cc_final: 0.8087 (tppp) REVERT: D 338 LYS cc_start: 0.7392 (pttm) cc_final: 0.6627 (pttm) outliers start: 78 outliers final: 43 residues processed: 592 average time/residue: 0.2782 time to fit residues: 224.7385 Evaluate side-chains 616 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 564 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR 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 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 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 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 206 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.128323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107353 restraints weight = 19699.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111483 restraints weight = 8937.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114217 restraints weight = 5061.855| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1832 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= 0.126 Angle : 0.509 7.961 17047 Z= 0.266 Chirality : 0.042 0.193 1916 Planarity : 0.004 0.061 2192 Dihedral : 4.198 50.848 1680 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.68 % Allowed : 29.84 % Favored : 64.47 % 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: 0.80 (0.21), residues: 674 sheet: 1.70 (0.44), residues: 149 loop : -0.77 (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 0.023 0.001 TYR A 118 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 454) hydrogen bonds : angle 4.18016 ( 1302) covalent geometry : bond 0.00285 (12586) covalent geometry : angle 0.50913 (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 636 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 560 time to evaluate : 1.238 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: 0.4085 (OUTLIER) cc_final: 0.1898 (p90) REVERT: E 60 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6271 (pm20) REVERT: E 194 ARG cc_start: 0.7206 (mtp-110) cc_final: 0.6701 (mtp-110) REVERT: E 197 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6840 (pm20) REVERT: E 241 LEU cc_start: 0.8432 (mm) cc_final: 0.8217 (mt) REVERT: E 297 ASN cc_start: 0.8449 (t0) cc_final: 0.8244 (t0) REVERT: E 308 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7920 (tt) REVERT: E 316 TYR cc_start: 0.7758 (m-10) cc_final: 0.7424 (m-10) REVERT: E 322 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: E 324 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6849 (pp) REVERT: A 67 ASN cc_start: 0.8442 (t0) cc_final: 0.8089 (t0) REVERT: A 124 MET cc_start: 0.7714 (mmt) cc_final: 0.7399 (mmt) REVERT: A 175 ASN cc_start: 0.8072 (m-40) cc_final: 0.7848 (m-40) REVERT: A 178 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7406 (mtmm) REVERT: A 191 VAL cc_start: 0.8631 (t) cc_final: 0.8365 (p) REVERT: A 237 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8345 (t) REVERT: A 248 HIS cc_start: 0.8735 (t-90) cc_final: 0.8496 (t-170) REVERT: A 329 LYS cc_start: 0.8146 (mttt) cc_final: 0.7581 (mttt) REVERT: B 47 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7848 (tm-30) REVERT: B 157 GLU cc_start: 0.7480 (tt0) cc_final: 0.7169 (tp30) REVERT: B 200 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8289 (mptt) REVERT: C 34 TYR cc_start: 0.7724 (t80) cc_final: 0.7228 (t80) REVERT: C 43 ARG cc_start: 0.7461 (tmm160) cc_final: 0.6970 (tmm160) REVERT: C 64 GLN cc_start: 0.8010 (tp40) cc_final: 0.7673 (tp40) REVERT: C 103 TYR cc_start: 0.8494 (p90) cc_final: 0.7983 (p90) REVERT: C 107 LEU cc_start: 0.8120 (mm) cc_final: 0.7770 (mp) REVERT: C 201 TRP cc_start: 0.7880 (OUTLIER) cc_final: 0.6622 (m-10) REVERT: C 215 ASN cc_start: 0.8453 (t0) cc_final: 0.8049 (t0) REVERT: C 338 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7508 (tmmt) REVERT: C 345 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8480 (mp) REVERT: C 354 THR cc_start: 0.7623 (p) cc_final: 0.7398 (p) REVERT: D 74 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8151 (mm) REVERT: D 114 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6811 (mm-30) REVERT: D 116 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8435 (tt) REVERT: D 166 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.5787 (mp) REVERT: D 180 GLU cc_start: 0.8005 (tt0) cc_final: 0.7781 (tt0) REVERT: D 213 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: D 338 LYS cc_start: 0.7392 (pttm) cc_final: 0.6776 (pttm) outliers start: 76 outliers final: 37 residues processed: 589 average time/residue: 0.2696 time to fit residues: 217.4954 Evaluate side-chains 598 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 546 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 308 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 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 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 296 MET Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 204 SER 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 166 ILE 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: 0.2980 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.0470 chunk 90 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.0370 chunk 143 optimal weight: 0.9980 overall best weight: 0.2556 ------------------------------------------------------------------------------- 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 C 123 ASN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111259 restraints weight = 20074.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115507 restraints weight = 9152.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118268 restraints weight = 5186.893| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12586 Z= 0.087 Angle : 0.482 9.440 17047 Z= 0.245 Chirality : 0.040 0.182 1916 Planarity : 0.004 0.058 2192 Dihedral : 3.826 44.105 1680 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.34 % Allowed : 31.34 % Favored : 64.32 % 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: 0.39 (0.22), residues: 1520 helix: 0.93 (0.21), residues: 671 sheet: 1.84 (0.44), residues: 152 loop : -0.75 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 201 HIS 0.003 0.000 HIS B 248 PHE 0.014 0.001 PHE D 312 TYR 0.024 0.001 TYR A 118 ARG 0.003 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 454) hydrogen bonds : angle 3.88466 ( 1302) covalent geometry : bond 0.00195 (12586) covalent geometry : angle 0.48160 (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 602 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 544 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4113 (OUTLIER) cc_final: 0.1898 (p90) REVERT: E 60 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6178 (pm20) REVERT: E 197 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6622 (pm20) REVERT: E 207 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8534 (mmmt) REVERT: E 227 ILE cc_start: 0.7757 (mm) cc_final: 0.7483 (mm) REVERT: E 297 ASN cc_start: 0.8414 (t0) cc_final: 0.7471 (t0) REVERT: E 300 LYS cc_start: 0.7976 (mttt) cc_final: 0.7672 (mttt) REVERT: E 316 TYR cc_start: 0.7781 (m-10) cc_final: 0.7489 (m-10) REVERT: E 322 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: E 324 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6838 (pp) REVERT: A 46 LEU cc_start: 0.8556 (mt) cc_final: 0.8283 (mp) REVERT: A 124 MET cc_start: 0.7685 (mmt) cc_final: 0.7326 (mmt) REVERT: A 175 ASN cc_start: 0.8030 (m-40) cc_final: 0.7735 (m-40) REVERT: A 178 LYS cc_start: 0.7999 (mtmm) cc_final: 0.7478 (mtmm) REVERT: A 191 VAL cc_start: 0.8547 (t) cc_final: 0.8287 (p) REVERT: A 266 ILE cc_start: 0.8716 (tt) cc_final: 0.8506 (tt) REVERT: A 269 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8489 (tp40) REVERT: A 329 LYS cc_start: 0.8135 (mttt) cc_final: 0.7578 (mttt) REVERT: B 47 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7733 (tm-30) REVERT: B 157 GLU cc_start: 0.7485 (tt0) cc_final: 0.7151 (tp30) REVERT: B 212 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8100 (tttp) REVERT: C 43 ARG cc_start: 0.7423 (tmm160) cc_final: 0.6951 (tmm160) REVERT: C 103 TYR cc_start: 0.8450 (p90) cc_final: 0.8173 (p90) REVERT: C 120 VAL cc_start: 0.8721 (t) cc_final: 0.8511 (t) REVERT: C 190 MET cc_start: 0.8620 (tpp) cc_final: 0.8310 (tpt) REVERT: C 215 ASN cc_start: 0.8479 (t0) cc_final: 0.8051 (t0) REVERT: C 256 VAL cc_start: 0.8546 (t) cc_final: 0.8312 (p) REVERT: C 354 THR cc_start: 0.7514 (p) cc_final: 0.7263 (p) REVERT: D 38 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7690 (mtp180) REVERT: D 103 TYR cc_start: 0.8357 (p90) cc_final: 0.7866 (p90) REVERT: D 114 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6804 (mm-30) REVERT: D 166 ILE cc_start: 0.6108 (OUTLIER) cc_final: 0.5797 (mp) REVERT: D 174 GLU cc_start: 0.8183 (tt0) cc_final: 0.7741 (tt0) REVERT: D 180 GLU cc_start: 0.7892 (tt0) cc_final: 0.7571 (tt0) REVERT: D 189 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: D 209 ARG cc_start: 0.8482 (tpp80) cc_final: 0.7852 (tpt90) REVERT: D 213 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: D 312 PHE cc_start: 0.7132 (p90) cc_final: 0.6866 (p90) REVERT: D 338 LYS cc_start: 0.7271 (pttm) cc_final: 0.6879 (pttm) outliers start: 58 outliers final: 30 residues processed: 568 average time/residue: 0.2579 time to fit residues: 201.8723 Evaluate side-chains 583 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 544 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 212 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 204 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 189 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 256 VAL Chi-restraints excluded: chain D residue 285 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 0.9980 chunk 127 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 114 optimal weight: 0.0570 chunk 72 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 55 GLN C 121 GLN C 123 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 294 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107310 restraints weight = 19984.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111239 restraints weight = 9549.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113865 restraints weight = 5569.763| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12586 Z= 0.098 Angle : 0.499 8.706 17047 Z= 0.253 Chirality : 0.041 0.201 1916 Planarity : 0.004 0.058 2192 Dihedral : 3.745 33.817 1680 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.11 % Allowed : 31.41 % Favored : 64.47 % 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: 0.45 (0.22), residues: 1520 helix: 0.97 (0.21), residues: 672 sheet: 1.92 (0.43), residues: 159 loop : -0.75 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 201 HIS 0.004 0.001 HIS E 80 PHE 0.012 0.001 PHE D 312 TYR 0.024 0.001 TYR A 118 ARG 0.006 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 454) hydrogen bonds : angle 3.88641 ( 1302) covalent geometry : bond 0.00227 (12586) covalent geometry : angle 0.49889 (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 596 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 541 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4093 (OUTLIER) cc_final: 0.1887 (p90) REVERT: E 60 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6241 (pm20) REVERT: E 151 LYS cc_start: 0.8371 (pttt) cc_final: 0.7967 (pttt) REVERT: E 197 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: E 207 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8468 (mmmt) REVERT: E 227 ILE cc_start: 0.7829 (mm) cc_final: 0.7556 (mm) REVERT: E 241 LEU cc_start: 0.8485 (mm) cc_final: 0.8167 (mt) REVERT: E 297 ASN cc_start: 0.8459 (t0) cc_final: 0.8250 (t0) REVERT: E 308 LEU cc_start: 0.8180 (tp) cc_final: 0.7795 (tt) REVERT: E 316 TYR cc_start: 0.7789 (m-10) cc_final: 0.7504 (m-10) REVERT: E 324 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6841 (pp) REVERT: A 46 LEU cc_start: 0.8574 (mt) cc_final: 0.8355 (mp) REVERT: A 124 MET cc_start: 0.7685 (mmt) cc_final: 0.7331 (mmt) REVERT: A 175 ASN cc_start: 0.8023 (m-40) cc_final: 0.7750 (m-40) REVERT: A 178 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7512 (mtmm) REVERT: A 191 VAL cc_start: 0.8561 (t) cc_final: 0.8287 (p) REVERT: A 266 ILE cc_start: 0.8754 (tt) cc_final: 0.8499 (tt) REVERT: A 281 LEU cc_start: 0.8008 (mp) cc_final: 0.7803 (mt) REVERT: A 329 LYS cc_start: 0.8129 (mttt) cc_final: 0.7596 (mttt) REVERT: B 47 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 157 GLU cc_start: 0.7495 (tt0) cc_final: 0.7167 (tp30) REVERT: C 43 ARG cc_start: 0.7451 (tmm160) cc_final: 0.6989 (tmm160) REVERT: C 103 TYR cc_start: 0.8480 (p90) cc_final: 0.8131 (p90) REVERT: C 136 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6922 (tm-30) REVERT: C 199 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8305 (t) REVERT: C 201 TRP cc_start: 0.7693 (OUTLIER) cc_final: 0.6434 (m-10) REVERT: C 215 ASN cc_start: 0.8504 (t0) cc_final: 0.8063 (t0) REVERT: C 256 VAL cc_start: 0.8559 (t) cc_final: 0.8331 (p) REVERT: D 38 ARG cc_start: 0.7965 (mtp180) cc_final: 0.7718 (mtp180) REVERT: D 114 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6817 (mm-30) REVERT: D 116 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8352 (tt) REVERT: D 166 ILE cc_start: 0.6084 (OUTLIER) cc_final: 0.5775 (mp) REVERT: D 174 GLU cc_start: 0.8187 (tt0) cc_final: 0.7739 (tt0) REVERT: D 180 GLU cc_start: 0.7926 (tt0) cc_final: 0.7552 (tt0) REVERT: D 213 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: D 338 LYS cc_start: 0.7339 (pttm) cc_final: 0.6903 (pttm) outliers start: 55 outliers final: 36 residues processed: 563 average time/residue: 0.2653 time to fit residues: 205.0118 Evaluate side-chains 585 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 540 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 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 225 GLN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain 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 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 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 256 VAL Chi-restraints excluded: chain D residue 285 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.0670 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.109903 restraints weight = 19826.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114122 restraints weight = 9102.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116888 restraints weight = 5181.557| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2217 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 : 0.505 8.651 17047 Z= 0.259 Chirality : 0.042 0.212 1916 Planarity : 0.004 0.057 2192 Dihedral : 3.744 27.388 1680 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.19 % Allowed : 31.49 % Favored : 64.32 % 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: 0.49 (0.22), residues: 1520 helix: 1.07 (0.21), residues: 656 sheet: 1.71 (0.43), residues: 165 loop : -0.72 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.004 0.001 HIS E 80 PHE 0.015 0.001 PHE C 355 TYR 0.024 0.001 TYR A 118 ARG 0.006 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 454) hydrogen bonds : angle 3.95508 ( 1302) covalent geometry : bond 0.00250 (12586) covalent geometry : angle 0.50536 (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 612 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 556 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4078 (OUTLIER) cc_final: 0.1909 (p90) REVERT: E 60 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6251 (pm20) REVERT: E 151 LYS cc_start: 0.8409 (pttt) cc_final: 0.7999 (pttt) REVERT: E 194 ARG cc_start: 0.7187 (mtp-110) cc_final: 0.6652 (mtp-110) REVERT: E 197 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6643 (pm20) REVERT: E 207 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8502 (mmmt) REVERT: E 227 ILE cc_start: 0.7852 (mm) cc_final: 0.7573 (mm) REVERT: E 241 LEU cc_start: 0.8439 (mm) cc_final: 0.8112 (mt) REVERT: E 297 ASN cc_start: 0.8464 (t0) cc_final: 0.8264 (t0) REVERT: E 308 LEU cc_start: 0.8273 (tp) cc_final: 0.8004 (tt) REVERT: E 316 TYR cc_start: 0.7733 (m-10) cc_final: 0.7432 (m-10) REVERT: E 324 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6727 (pp) REVERT: A 46 LEU cc_start: 0.8590 (mt) cc_final: 0.8373 (mp) REVERT: A 67 ASN cc_start: 0.8473 (t0) cc_final: 0.8146 (t0) REVERT: A 124 MET cc_start: 0.7712 (mmt) cc_final: 0.7356 (mmt) REVERT: A 175 ASN cc_start: 0.8033 (m-40) cc_final: 0.7787 (m-40) REVERT: A 178 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7563 (mtmm) REVERT: A 191 VAL cc_start: 0.8558 (t) cc_final: 0.8273 (p) REVERT: A 281 LEU cc_start: 0.7998 (mp) cc_final: 0.7798 (mt) REVERT: A 329 LYS cc_start: 0.8094 (mttt) cc_final: 0.7539 (mttt) REVERT: B 47 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 157 GLU cc_start: 0.7486 (tt0) cc_final: 0.7169 (tp30) REVERT: B 175 ASN cc_start: 0.8649 (m-40) cc_final: 0.8411 (m110) REVERT: C 43 ARG cc_start: 0.7475 (tmm160) cc_final: 0.7002 (tmm160) REVERT: C 103 TYR cc_start: 0.8473 (p90) cc_final: 0.8131 (p90) REVERT: C 136 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6926 (tm-30) REVERT: C 199 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8384 (t) REVERT: C 201 TRP cc_start: 0.7831 (OUTLIER) cc_final: 0.6760 (m-10) REVERT: C 215 ASN cc_start: 0.8519 (t0) cc_final: 0.8066 (t0) REVERT: C 256 VAL cc_start: 0.8577 (t) cc_final: 0.8361 (p) REVERT: C 287 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8412 (ttmt) REVERT: C 354 THR cc_start: 0.7383 (p) cc_final: 0.7146 (p) REVERT: D 38 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7734 (mtp180) REVERT: D 64 GLN cc_start: 0.7677 (tt0) cc_final: 0.7471 (tp40) REVERT: D 114 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6818 (mm-30) REVERT: D 116 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8422 (tt) REVERT: D 166 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5813 (mp) REVERT: D 174 GLU cc_start: 0.8179 (tt0) cc_final: 0.7712 (tt0) REVERT: D 180 GLU cc_start: 0.7924 (tt0) cc_final: 0.7563 (tt0) REVERT: D 209 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8075 (tpt-90) REVERT: D 213 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: D 338 LYS cc_start: 0.7371 (pttm) cc_final: 0.6781 (pttm) outliers start: 56 outliers final: 37 residues processed: 576 average time/residue: 0.2693 time to fit residues: 213.5814 Evaluate side-chains 600 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 554 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 197 GLU 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 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 345 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 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain 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 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 344 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 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 256 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 72 optimal weight: 0.1980 chunk 93 optimal weight: 0.4980 chunk 115 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 96 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 80 HIS E 238 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 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 = 0.3671 r_free = 0.3671 target = 0.130571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109799 restraints weight = 19909.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113819 restraints weight = 9397.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116484 restraints weight = 5456.811| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12586 Z= 0.096 Angle : 0.512 9.911 17047 Z= 0.259 Chirality : 0.041 0.212 1916 Planarity : 0.004 0.058 2192 Dihedral : 3.664 27.551 1679 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.74 % Allowed : 31.94 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1520 helix: 0.97 (0.21), residues: 664 sheet: 1.69 (0.43), residues: 165 loop : -0.70 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.003 0.001 HIS B 248 PHE 0.013 0.001 PHE D 312 TYR 0.025 0.001 TYR A 118 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 454) hydrogen bonds : angle 3.92130 ( 1302) covalent geometry : bond 0.00224 (12586) covalent geometry : angle 0.51236 (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 596 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 546 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4038 (OUTLIER) cc_final: 0.1892 (p90) REVERT: E 60 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6140 (pm20) REVERT: E 151 LYS cc_start: 0.8403 (pttt) cc_final: 0.7968 (pttt) REVERT: E 194 ARG cc_start: 0.7184 (mtp-110) cc_final: 0.6627 (mtp-110) REVERT: E 197 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6542 (pm20) REVERT: E 207 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8434 (mmmt) REVERT: E 227 ILE cc_start: 0.7786 (mm) cc_final: 0.7503 (mm) REVERT: E 241 LEU cc_start: 0.8466 (mm) cc_final: 0.8147 (mt) REVERT: E 297 ASN cc_start: 0.8453 (t0) cc_final: 0.8237 (t0) REVERT: E 308 LEU cc_start: 0.8237 (tp) cc_final: 0.7942 (tt) REVERT: E 316 TYR cc_start: 0.7798 (m-10) cc_final: 0.7499 (m-10) REVERT: A 67 ASN cc_start: 0.8453 (t0) cc_final: 0.8135 (t0) REVERT: A 124 MET cc_start: 0.7733 (mmt) cc_final: 0.7347 (mmt) REVERT: A 175 ASN cc_start: 0.8016 (m-40) cc_final: 0.7775 (m-40) REVERT: A 178 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7534 (mtmm) REVERT: A 213 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7713 (mm-30) REVERT: A 329 LYS cc_start: 0.8070 (mttt) cc_final: 0.7496 (mttt) REVERT: B 47 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 157 GLU cc_start: 0.7489 (tt0) cc_final: 0.7157 (tp30) REVERT: B 175 ASN cc_start: 0.8686 (m-40) cc_final: 0.8428 (m110) REVERT: B 212 LYS cc_start: 0.8080 (tttp) cc_final: 0.7704 (ttmp) REVERT: B 247 PHE cc_start: 0.8939 (m-80) cc_final: 0.8717 (m-80) REVERT: B 267 ASN cc_start: 0.8294 (m-40) cc_final: 0.7970 (m-40) REVERT: C 43 ARG cc_start: 0.7460 (tmm160) cc_final: 0.7022 (tmm160) REVERT: C 103 TYR cc_start: 0.8454 (p90) cc_final: 0.8160 (p90) REVERT: C 136 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6912 (tm-30) REVERT: C 201 TRP cc_start: 0.7751 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: C 215 ASN cc_start: 0.8515 (t0) cc_final: 0.8050 (t0) REVERT: C 256 VAL cc_start: 0.8586 (t) cc_final: 0.8341 (p) REVERT: C 264 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.6935 (ttm-80) REVERT: C 287 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8401 (ttmt) REVERT: D 38 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7694 (mtp180) REVERT: D 64 GLN cc_start: 0.7690 (tt0) cc_final: 0.7484 (tp40) REVERT: D 103 TYR cc_start: 0.8368 (p90) cc_final: 0.7849 (p90) REVERT: D 114 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6820 (mm-30) REVERT: D 116 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8334 (tt) REVERT: D 166 ILE cc_start: 0.6090 (OUTLIER) cc_final: 0.5790 (mp) REVERT: D 174 GLU cc_start: 0.8180 (tt0) cc_final: 0.7716 (tt0) REVERT: D 180 GLU cc_start: 0.7921 (tt0) cc_final: 0.7519 (tt0) REVERT: D 209 ARG cc_start: 0.8520 (tpp80) cc_final: 0.7937 (tpt90) REVERT: D 213 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: D 338 LYS cc_start: 0.7358 (pttm) cc_final: 0.6869 (pttm) outliers start: 50 outliers final: 38 residues processed: 564 average time/residue: 0.3093 time to fit residues: 241.0430 Evaluate side-chains 587 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 542 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 197 GLU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 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 260 VAL Chi-restraints excluded: chain A residue 345 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 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 ILE 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 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 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 138 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN A 121 GLN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109576 restraints weight = 19669.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113782 restraints weight = 9055.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116527 restraints weight = 5156.829| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12586 Z= 0.117 Angle : 0.530 9.203 17047 Z= 0.270 Chirality : 0.042 0.224 1916 Planarity : 0.004 0.056 2192 Dihedral : 3.745 27.967 1679 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.74 % Allowed : 32.24 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1520 helix: 1.00 (0.21), residues: 657 sheet: 1.68 (0.43), residues: 165 loop : -0.70 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 201 HIS 0.004 0.001 HIS E 80 PHE 0.014 0.001 PHE C 355 TYR 0.025 0.001 TYR A 118 ARG 0.005 0.000 ARG E 77 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 454) hydrogen bonds : angle 3.98262 ( 1302) covalent geometry : bond 0.00271 (12586) covalent geometry : angle 0.53027 (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 603 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 553 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4094 (OUTLIER) cc_final: 0.1932 (p90) REVERT: E 60 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6178 (pm20) REVERT: E 151 LYS cc_start: 0.8432 (pttt) cc_final: 0.8003 (pttt) REVERT: E 197 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6546 (pm20) REVERT: E 227 ILE cc_start: 0.7850 (mm) cc_final: 0.7579 (mm) REVERT: E 241 LEU cc_start: 0.8430 (mm) cc_final: 0.8119 (mt) REVERT: E 308 LEU cc_start: 0.8244 (tp) cc_final: 0.7926 (tp) REVERT: E 316 TYR cc_start: 0.7796 (m-10) cc_final: 0.7492 (m-10) REVERT: A 67 ASN cc_start: 0.8499 (t0) cc_final: 0.8160 (t0) REVERT: A 124 MET cc_start: 0.7742 (mmt) cc_final: 0.7351 (mmt) REVERT: A 175 ASN cc_start: 0.8059 (m-40) cc_final: 0.7802 (m-40) REVERT: A 178 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7567 (mtmm) REVERT: A 213 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 329 LYS cc_start: 0.8065 (mttt) cc_final: 0.7516 (mttt) REVERT: B 47 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 157 GLU cc_start: 0.7480 (tt0) cc_final: 0.7161 (tp30) REVERT: B 175 ASN cc_start: 0.8668 (m-40) cc_final: 0.8412 (m110) REVERT: B 212 LYS cc_start: 0.8099 (tttp) cc_final: 0.7759 (ttmp) REVERT: B 247 PHE cc_start: 0.8927 (m-80) cc_final: 0.8658 (m-80) REVERT: C 43 ARG cc_start: 0.7458 (tmm160) cc_final: 0.7039 (tmm160) REVERT: C 64 GLN cc_start: 0.8011 (tp40) cc_final: 0.7700 (tp40) REVERT: C 103 TYR cc_start: 0.8457 (p90) cc_final: 0.8008 (p90) REVERT: C 136 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6939 (tm-30) REVERT: C 199 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8455 (t) REVERT: C 201 TRP cc_start: 0.7778 (OUTLIER) cc_final: 0.6758 (m-10) REVERT: C 215 ASN cc_start: 0.8509 (t0) cc_final: 0.8083 (t0) REVERT: C 216 ASN cc_start: 0.8216 (t0) cc_final: 0.7750 (t0) REVERT: C 256 VAL cc_start: 0.8599 (t) cc_final: 0.8365 (p) REVERT: D 38 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7729 (mtp180) REVERT: D 64 GLN cc_start: 0.7682 (tt0) cc_final: 0.7477 (tp40) REVERT: D 114 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6826 (mm-30) REVERT: D 116 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8420 (tt) REVERT: D 166 ILE cc_start: 0.6126 (OUTLIER) cc_final: 0.5821 (mp) REVERT: D 174 GLU cc_start: 0.8159 (tt0) cc_final: 0.7711 (tt0) REVERT: D 180 GLU cc_start: 0.7896 (tt0) cc_final: 0.7514 (tt0) REVERT: D 213 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: D 294 ASN cc_start: 0.7772 (t0) cc_final: 0.7569 (t0) REVERT: D 338 LYS cc_start: 0.7388 (pttm) cc_final: 0.6886 (pttm) outliers start: 50 outliers final: 37 residues processed: 571 average time/residue: 0.2697 time to fit residues: 211.2499 Evaluate side-chains 598 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 553 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 197 GLU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain 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 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 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 256 VAL Chi-restraints excluded: chain D residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 123 ASN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110334 restraints weight = 19751.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114592 restraints weight = 9078.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117347 restraints weight = 5163.854| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2393 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= 0.103 Angle : 0.518 8.371 17047 Z= 0.263 Chirality : 0.042 0.220 1916 Planarity : 0.004 0.056 2192 Dihedral : 3.719 28.177 1679 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.96 % Allowed : 32.09 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1520 helix: 1.00 (0.21), residues: 657 sheet: 1.63 (0.43), residues: 165 loop : -0.68 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 201 HIS 0.005 0.001 HIS E 80 PHE 0.012 0.001 PHE D 312 TYR 0.026 0.001 TYR A 118 ARG 0.005 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 454) hydrogen bonds : angle 3.93733 ( 1302) covalent geometry : bond 0.00239 (12586) covalent geometry : angle 0.51782 (17047) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5120.40 seconds wall clock time: 89 minutes 14.63 seconds (5354.63 seconds total)