Starting phenix.real_space_refine on Sat Aug 23 21:03:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ud6_64063/08_2025/9ud6_64063.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ud6_64063/08_2025/9ud6_64063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ud6_64063/08_2025/9ud6_64063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ud6_64063/08_2025/9ud6_64063.map" model { file = "/net/cci-nas-00/data/ceres_data/9ud6_64063/08_2025/9ud6_64063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ud6_64063/08_2025/9ud6_64063.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 4 5.49 5 S 92 5.16 5 C 9532 2.51 5 N 2409 2.21 5 O 2701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14743 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} Chain: "B" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2964 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3165 Classifications: {'peptide': 408} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 380} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'FMN': 1, 'LMT': 1, 'RBF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9088 SG CYS D 112 43.238 74.024 66.818 1.00 94.04 S ATOM 10054 SG CYS E 26 45.021 71.200 67.845 1.00 94.70 S ATOM 8449 SG CYS D 29 43.911 68.224 63.706 1.00 91.95 S ATOM 10776 SG CYS E 120 42.131 71.089 62.001 1.00103.33 S ATOM 11902 SG CYS F 79 39.358 89.979 94.112 1.00227.27 S ATOM 11855 SG CYS F 70 44.475 92.671 90.456 1.00249.43 S Time building chain proxies: 2.92, per 1000 atoms: 0.20 Number of scatterers: 14743 At special positions: 0 Unit cell: (88.88, 124.96, 154.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 4 15.00 O 2701 8.00 N 2409 7.00 C 9532 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: 0.92 Conformation dependent library (CDL) restraints added in 480.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 70 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 79 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 111 " Number of angles added : 10 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 13 sheets defined 56.2% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.512A pdb=" N LEU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 106 through 111' Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.661A pdb=" N PHE A 131 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.571A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.645A pdb=" N THR A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.554A pdb=" N MET A 339 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.823A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 445 removed outlier: 4.033A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 35 Processing helix chain 'B' and resid 52 through 63 Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 152 removed outlier: 3.656A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.519A pdb=" N ALA B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.671A pdb=" N GLU B 274 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 275 " --> pdb=" O ILE B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.858A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.663A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.961A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 333 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.826A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.698A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.585A pdb=" N ILE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 54 removed outlier: 3.532A pdb=" N ALA C 41 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 4.154A pdb=" N GLN C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.518A pdb=" N TYR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.881A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'D' and resid 8 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.635A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.503A pdb=" N ILE D 66 " --> pdb=" O ARG D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 94 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.346A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.817A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.615A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.574A pdb=" N LEU D 182 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 202 removed outlier: 3.845A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 113 through 117 removed outlier: 3.591A pdb=" N THR E 117 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.975A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 Processing helix chain 'F' and resid 54 through 63 Processing helix chain 'F' and resid 91 through 96 removed outlier: 4.016A pdb=" N LEU F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 91 through 96' Processing helix chain 'F' and resid 99 through 104 removed outlier: 3.701A pdb=" N ARG F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 130 Processing helix chain 'F' and resid 155 through 158 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 188 through 196 removed outlier: 4.274A pdb=" N TRP F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.753A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 removed outlier: 3.814A pdb=" N MET F 317 " --> pdb=" O LYS F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 343 through 347 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 364 through 367 Processing helix chain 'F' and resid 380 through 395 Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.637A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 8.300A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.618A pdb=" N ASN A 80 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 90 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU A 78 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 92 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 76 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 94 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY A 74 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.084A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 84 removed outlier: 4.432A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.687A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.592A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.328A pdb=" N LYS C 204 " --> pdb=" O VAL C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'F' and resid 46 through 49 removed outlier: 6.779A pdb=" N THR F 36 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP F 120 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 208 through 213 removed outlier: 6.975A pdb=" N GLN F 169 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY F 262 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU F 171 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE F 260 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY F 262 " --> pdb=" O LYS F 131 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS F 131 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL F 137 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA F 153 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER F 139 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 176 through 178 Processing sheet with id=AB4, first strand: chain 'F' and resid 333 through 339 removed outlier: 6.890A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY F 281 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 6071 1.40 - 1.60: 8841 1.60 - 1.80: 126 1.80 - 2.00: 35 2.00 - 2.20: 8 Bond restraints: 15081 Sorted by residual: bond pdb=" C4 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.402 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.404 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" O5' FMN C 301 " pdb=" P FMN C 301 " ideal model delta sigma weight residual 1.676 1.609 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O5' FMN B 501 " pdb=" P FMN B 501 " ideal model delta sigma weight residual 1.676 1.611 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C2 FMN C 301 " pdb=" N3 FMN C 301 " ideal model delta sigma weight residual 1.404 1.351 0.053 2.00e-02 2.50e+03 6.90e+00 ... (remaining 15076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 20196 2.26 - 4.51: 262 4.51 - 6.77: 8 6.77 - 9.02: 1 9.02 - 11.28: 1 Bond angle restraints: 20468 Sorted by residual: angle pdb=" C VAL F 66 " pdb=" N SER F 67 " pdb=" CA SER F 67 " ideal model delta sigma weight residual 121.70 132.98 -11.28 1.80e+00 3.09e-01 3.92e+01 angle pdb=" C GLY F 77 " pdb=" N GLN F 78 " pdb=" CA GLN F 78 " ideal model delta sigma weight residual 121.70 127.25 -5.55 1.80e+00 3.09e-01 9.50e+00 angle pdb=" CA VAL F 66 " pdb=" C VAL F 66 " pdb=" N SER F 67 " ideal model delta sigma weight residual 116.84 120.16 -3.32 1.09e+00 8.42e-01 9.30e+00 angle pdb=" N SER F 67 " pdb=" CA SER F 67 " pdb=" C SER F 67 " ideal model delta sigma weight residual 111.00 119.53 -8.53 2.80e+00 1.28e-01 9.28e+00 angle pdb=" CA TRP B 103 " pdb=" CB TRP B 103 " pdb=" CG TRP B 103 " ideal model delta sigma weight residual 113.60 119.11 -5.51 1.90e+00 2.77e-01 8.41e+00 ... (remaining 20463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8189 17.97 - 35.93: 592 35.93 - 53.90: 133 53.90 - 71.87: 27 71.87 - 89.84: 13 Dihedral angle restraints: 8954 sinusoidal: 3592 harmonic: 5362 Sorted by residual: dihedral pdb=" CA SER F 67 " pdb=" C SER F 67 " pdb=" N SER F 68 " pdb=" CA SER F 68 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ARG B 43 " pdb=" C ARG B 43 " pdb=" N SER B 44 " pdb=" CA SER B 44 " ideal model delta harmonic sigma weight residual 180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA TYR F 217 " pdb=" C TYR F 217 " pdb=" N PRO F 218 " pdb=" CA PRO F 218 " ideal model delta harmonic sigma weight residual -180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 8951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1675 0.041 - 0.082: 422 0.082 - 0.123: 210 0.123 - 0.164: 12 0.164 - 0.205: 1 Chirality restraints: 2320 Sorted by residual: chirality pdb=" CA SER F 67 " pdb=" N SER F 67 " pdb=" C SER F 67 " pdb=" CB SER F 67 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB THR C 11 " pdb=" CA THR C 11 " pdb=" OG1 THR C 11 " pdb=" CG2 THR C 11 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA TRP B 103 " pdb=" N TRP B 103 " pdb=" C TRP B 103 " pdb=" CB TRP B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 2317 not shown) Planarity restraints: 2567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 128 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO D 129 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 129 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 129 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 174 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B 175 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 203 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO B 204 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " 0.019 5.00e-02 4.00e+02 ... (remaining 2564 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 129 2.62 - 3.19: 13301 3.19 - 3.76: 21839 3.76 - 4.33: 32240 4.33 - 4.90: 53610 Nonbonded interactions: 121119 Sorted by model distance: nonbonded pdb=" O HOH D 401 " pdb=" O HOH D 402 " model vdw 2.055 3.040 nonbonded pdb=" O PRO F 31 " pdb=" OG1 THR F 32 " model vdw 2.092 3.040 nonbonded pdb=" O2P FMN B 501 " pdb=" O4' FMN B 501 " model vdw 2.097 3.040 nonbonded pdb=" O2B LMT D 301 " pdb=" O6' LMT D 301 " model vdw 2.150 3.040 nonbonded pdb=" O PRO F 241 " pdb=" O2B FAD F 502 " model vdw 2.164 3.040 ... (remaining 121114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.360 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 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 : 0.008 0.885 15088 Z= 0.237 Angle : 0.606 23.152 20478 Z= 0.299 Chirality : 0.044 0.205 2320 Planarity : 0.004 0.040 2567 Dihedral : 13.840 89.836 5534 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.58 % Allowed : 8.93 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.19), residues: 1882 helix: 1.96 (0.18), residues: 862 sheet: 0.34 (0.40), residues: 166 loop : -0.18 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 43 TYR 0.015 0.001 TYR D 141 PHE 0.016 0.001 PHE F 221 TRP 0.018 0.001 TRP B 103 HIS 0.002 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00379 (15081) covalent geometry : angle 0.55813 (20468) hydrogen bonds : bond 0.12519 ( 744) hydrogen bonds : angle 5.51000 ( 2103) metal coordination : bond 0.33469 ( 7) metal coordination : angle 10.74966 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 300 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5002 (ttp) cc_final: 0.4334 (mtp) REVERT: A 46 ARG cc_start: 0.6338 (ptp90) cc_final: 0.6059 (mtm110) REVERT: A 50 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7710 (tp30) REVERT: A 59 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6831 (mt-10) REVERT: A 62 LYS cc_start: 0.7011 (mmmt) cc_final: 0.6222 (mmtm) REVERT: A 75 LYS cc_start: 0.7237 (ttmm) cc_final: 0.7026 (ttmt) REVERT: A 200 ARG cc_start: 0.6954 (mtp-110) cc_final: 0.6727 (mtp-110) REVERT: A 205 ASN cc_start: 0.6761 (m110) cc_final: 0.6527 (m110) REVERT: A 271 LYS cc_start: 0.6065 (ttmm) cc_final: 0.5855 (mttt) REVERT: A 284 GLU cc_start: 0.6497 (tt0) cc_final: 0.4988 (mp0) REVERT: A 291 ILE cc_start: 0.6790 (pt) cc_final: 0.6396 (mm) REVERT: A 344 LYS cc_start: 0.7245 (mttt) cc_final: 0.7024 (mttp) REVERT: A 444 LYS cc_start: 0.5152 (OUTLIER) cc_final: 0.4777 (ttpt) REVERT: B 43 ARG cc_start: 0.5253 (tpp80) cc_final: 0.4850 (mpp-170) REVERT: B 113 SER cc_start: 0.7059 (m) cc_final: 0.6507 (p) REVERT: B 406 LYS cc_start: 0.5908 (ttmm) cc_final: 0.5144 (mtmt) REVERT: C 45 LYS cc_start: 0.5251 (ttpt) cc_final: 0.4765 (tppt) REVERT: C 47 SER cc_start: 0.5624 (t) cc_final: 0.5399 (p) REVERT: C 48 LYS cc_start: 0.5203 (mmmt) cc_final: 0.4530 (mttm) REVERT: C 65 GLU cc_start: 0.6018 (tt0) cc_final: 0.5799 (tt0) REVERT: C 68 ASN cc_start: 0.6820 (m-40) cc_final: 0.6583 (m-40) REVERT: C 74 ARG cc_start: 0.6978 (mmm-85) cc_final: 0.6681 (mmm160) REVERT: C 77 ASP cc_start: 0.5945 (t0) cc_final: 0.5673 (t70) REVERT: C 85 GLU cc_start: 0.7193 (mp0) cc_final: 0.6779 (mp0) REVERT: C 95 LYS cc_start: 0.5456 (mtpt) cc_final: 0.5176 (mttm) REVERT: C 99 GLU cc_start: 0.3506 (mm-30) cc_final: 0.3287 (mm-30) REVERT: C 112 LYS cc_start: 0.5957 (mmtp) cc_final: 0.5611 (mttp) REVERT: C 156 GLU cc_start: 0.7189 (tp30) cc_final: 0.6364 (mm-30) REVERT: C 204 LYS cc_start: 0.5489 (mmtp) cc_final: 0.5229 (mmtm) REVERT: C 215 GLU cc_start: 0.6277 (pm20) cc_final: 0.5432 (pt0) REVERT: D 49 MET cc_start: 0.6371 (mtp) cc_final: 0.6102 (mtm) REVERT: D 99 LYS cc_start: 0.5689 (mtmt) cc_final: 0.5417 (mtpt) REVERT: D 207 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6669 (mt-10) REVERT: E 51 ILE cc_start: 0.6385 (mm) cc_final: 0.6111 (mt) REVERT: E 92 GLN cc_start: 0.4980 (mt0) cc_final: 0.4720 (mt0) REVERT: E 197 GLN cc_start: 0.6596 (pt0) cc_final: 0.5163 (mm-40) REVERT: F 199 ARG cc_start: 0.6191 (ptt-90) cc_final: 0.5897 (ptt90) REVERT: F 276 MET cc_start: 0.5599 (mtm) cc_final: 0.5355 (mtm) REVERT: F 289 ARG cc_start: 0.4949 (ttt-90) cc_final: 0.4582 (ttt-90) REVERT: F 314 LYS cc_start: 0.5866 (tttt) cc_final: 0.5517 (tppt) REVERT: F 329 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6674 (mt-10) REVERT: F 346 ASP cc_start: 0.4161 (m-30) cc_final: 0.3630 (m-30) REVERT: F 368 GLU cc_start: 0.6179 (mt-10) cc_final: 0.5769 (tt0) REVERT: F 374 GLU cc_start: 0.6010 (mt-10) cc_final: 0.5519 (mp0) outliers start: 9 outliers final: 4 residues processed: 306 average time/residue: 0.5916 time to fit residues: 197.2958 Evaluate side-chains 238 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 233 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 131 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0020 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 433 GLN B 243 GLN D 100 GLN F 362 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.184323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.128533 restraints weight = 12366.316| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.62 r_work: 0.3045 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15088 Z= 0.193 Angle : 0.669 13.594 20478 Z= 0.341 Chirality : 0.048 0.251 2320 Planarity : 0.005 0.058 2567 Dihedral : 6.872 74.669 2228 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.98 % Allowed : 10.55 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.19), residues: 1882 helix: 1.54 (0.18), residues: 862 sheet: 0.56 (0.40), residues: 164 loop : -0.39 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 318 TYR 0.016 0.002 TYR D 141 PHE 0.023 0.002 PHE B 159 TRP 0.023 0.002 TRP B 103 HIS 0.006 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00454 (15081) covalent geometry : angle 0.64694 (20468) hydrogen bonds : bond 0.06067 ( 744) hydrogen bonds : angle 4.92069 ( 2103) metal coordination : bond 0.01477 ( 7) metal coordination : angle 7.69702 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6041 (ttp) cc_final: 0.5418 (mtp) REVERT: A 46 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7416 (mtp-110) REVERT: A 50 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8097 (tp30) REVERT: A 59 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8006 (mt-10) REVERT: A 62 LYS cc_start: 0.8458 (mmmt) cc_final: 0.7548 (mtmt) REVERT: A 235 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7933 (t) REVERT: A 284 GLU cc_start: 0.7910 (tt0) cc_final: 0.6871 (mp0) REVERT: A 363 MET cc_start: 0.8803 (mtt) cc_final: 0.8562 (mtt) REVERT: B 43 ARG cc_start: 0.6951 (tpp80) cc_final: 0.6624 (tpp-160) REVERT: B 144 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8044 (mm-30) REVERT: B 380 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8414 (tp30) REVERT: B 406 LYS cc_start: 0.8333 (ttmm) cc_final: 0.7476 (mtmt) REVERT: C 48 LYS cc_start: 0.7369 (mmmt) cc_final: 0.6770 (mttp) REVERT: C 68 ASN cc_start: 0.8042 (m-40) cc_final: 0.7774 (m-40) REVERT: C 85 GLU cc_start: 0.7489 (mp0) cc_final: 0.7254 (mp0) REVERT: C 95 LYS cc_start: 0.7178 (mtpt) cc_final: 0.6815 (mttm) REVERT: C 99 GLU cc_start: 0.5489 (mm-30) cc_final: 0.5243 (mm-30) REVERT: C 109 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: C 156 GLU cc_start: 0.8091 (tp30) cc_final: 0.7589 (mm-30) REVERT: C 165 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8354 (tt) REVERT: C 215 GLU cc_start: 0.6972 (pm20) cc_final: 0.6408 (pt0) REVERT: D 17 ASP cc_start: 0.8319 (m-30) cc_final: 0.8055 (m-30) REVERT: D 49 MET cc_start: 0.8474 (mtp) cc_final: 0.8208 (mtm) REVERT: D 99 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7743 (mtpt) REVERT: D 207 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8002 (mt-10) REVERT: E 33 LYS cc_start: 0.8253 (mttt) cc_final: 0.7695 (mtmt) REVERT: E 51 ILE cc_start: 0.8331 (mm) cc_final: 0.8041 (mt) REVERT: E 92 GLN cc_start: 0.7403 (mt0) cc_final: 0.6991 (mt0) REVERT: E 197 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: F 80 ARG cc_start: 0.4391 (mtt-85) cc_final: 0.3634 (ptp90) REVERT: F 199 ARG cc_start: 0.6333 (ptt-90) cc_final: 0.6063 (ptt90) REVERT: F 289 ARG cc_start: 0.5370 (ttt-90) cc_final: 0.4798 (tmt170) REVERT: F 309 TYR cc_start: 0.5674 (t80) cc_final: 0.5448 (t80) REVERT: F 317 MET cc_start: 0.6759 (mtt) cc_final: 0.6419 (mmt) outliers start: 46 outliers final: 20 residues processed: 252 average time/residue: 0.5595 time to fit residues: 154.3042 Evaluate side-chains 231 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 145 optimal weight: 5.9990 chunk 128 optimal weight: 0.0570 chunk 127 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 433 GLN F 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.187327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.131998 restraints weight = 12472.038| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.58 r_work: 0.3089 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15088 Z= 0.123 Angle : 0.542 13.530 20478 Z= 0.282 Chirality : 0.043 0.232 2320 Planarity : 0.004 0.042 2567 Dihedral : 6.293 66.384 2224 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.72 % Allowed : 12.10 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 1882 helix: 1.69 (0.18), residues: 863 sheet: 0.62 (0.40), residues: 166 loop : -0.42 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 43 TYR 0.015 0.001 TYR D 141 PHE 0.018 0.001 PHE D 50 TRP 0.022 0.002 TRP B 103 HIS 0.005 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00267 (15081) covalent geometry : angle 0.52974 (20468) hydrogen bonds : bond 0.04752 ( 744) hydrogen bonds : angle 4.64797 ( 2103) metal coordination : bond 0.01390 ( 7) metal coordination : angle 5.29475 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6003 (ttp) cc_final: 0.5402 (mtp) REVERT: A 46 ARG cc_start: 0.7792 (ptp90) cc_final: 0.7323 (mtp180) REVERT: A 50 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8028 (mp0) REVERT: A 59 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 200 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7804 (mtp180) REVERT: A 349 ARG cc_start: 0.8816 (mtm-85) cc_final: 0.8476 (mtm-85) REVERT: A 363 MET cc_start: 0.8836 (mtt) cc_final: 0.8583 (mtt) REVERT: B 380 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: B 406 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7584 (mtmt) REVERT: C 45 LYS cc_start: 0.6959 (ttpt) cc_final: 0.6412 (tppt) REVERT: C 48 LYS cc_start: 0.7369 (mmmt) cc_final: 0.6838 (mttm) REVERT: C 68 ASN cc_start: 0.8058 (m-40) cc_final: 0.7828 (m-40) REVERT: C 85 GLU cc_start: 0.7508 (mp0) cc_final: 0.7217 (mp0) REVERT: C 95 LYS cc_start: 0.7164 (mtpt) cc_final: 0.6797 (mttm) REVERT: C 99 GLU cc_start: 0.5602 (mm-30) cc_final: 0.5295 (mm-30) REVERT: C 156 GLU cc_start: 0.8000 (tp30) cc_final: 0.7642 (mm-30) REVERT: C 215 GLU cc_start: 0.7041 (pm20) cc_final: 0.6461 (pt0) REVERT: D 17 ASP cc_start: 0.8326 (m-30) cc_final: 0.8027 (m-30) REVERT: D 49 MET cc_start: 0.8408 (mtp) cc_final: 0.8138 (mtm) REVERT: D 99 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7744 (mtpt) REVERT: E 33 LYS cc_start: 0.8256 (mttt) cc_final: 0.7696 (mtmt) REVERT: E 51 ILE cc_start: 0.8311 (mm) cc_final: 0.8021 (mt) REVERT: E 92 GLN cc_start: 0.7403 (mt0) cc_final: 0.6952 (mt0) REVERT: E 190 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7789 (t80) REVERT: E 197 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: F 80 ARG cc_start: 0.4375 (mtt-85) cc_final: 0.3734 (ptp90) REVERT: F 288 MET cc_start: 0.4781 (mmp) cc_final: 0.4552 (mmp) REVERT: F 289 ARG cc_start: 0.5344 (ttt-90) cc_final: 0.4803 (ttt-90) REVERT: F 303 ARG cc_start: 0.4701 (mtp180) cc_final: 0.4345 (mtp180) REVERT: F 317 MET cc_start: 0.6637 (mtt) cc_final: 0.6271 (mmt) outliers start: 42 outliers final: 15 residues processed: 236 average time/residue: 0.6811 time to fit residues: 174.5354 Evaluate side-chains 221 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 128 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 433 GLN D 24 GLN D 100 GLN F 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.186751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130839 restraints weight = 12396.794| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.64 r_work: 0.3093 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15088 Z= 0.138 Angle : 0.559 13.448 20478 Z= 0.292 Chirality : 0.044 0.232 2320 Planarity : 0.005 0.045 2567 Dihedral : 6.376 59.733 2223 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.98 % Allowed : 12.82 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.19), residues: 1882 helix: 1.63 (0.18), residues: 862 sheet: 0.67 (0.40), residues: 166 loop : -0.44 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 229 TYR 0.015 0.001 TYR D 141 PHE 0.018 0.002 PHE F 11 TRP 0.021 0.002 TRP B 103 HIS 0.004 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00309 (15081) covalent geometry : angle 0.55055 (20468) hydrogen bonds : bond 0.05027 ( 744) hydrogen bonds : angle 4.62764 ( 2103) metal coordination : bond 0.01172 ( 7) metal coordination : angle 4.46469 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6020 (ttp) cc_final: 0.5407 (mtp) REVERT: A 46 ARG cc_start: 0.7868 (ptp90) cc_final: 0.7400 (mtp180) REVERT: A 50 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8059 (mp0) REVERT: A 59 GLU cc_start: 0.8226 (mt-10) cc_final: 0.8015 (mt-10) REVERT: A 349 ARG cc_start: 0.8822 (mtm-85) cc_final: 0.8569 (mtm-85) REVERT: A 363 MET cc_start: 0.8823 (mtt) cc_final: 0.8575 (mtt) REVERT: A 384 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7250 (tmm) REVERT: A 433 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7930 (mm110) REVERT: B 380 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: B 406 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7518 (mtmt) REVERT: C 45 LYS cc_start: 0.7047 (ttpt) cc_final: 0.6473 (tppt) REVERT: C 48 LYS cc_start: 0.7382 (mmmt) cc_final: 0.6851 (mttm) REVERT: C 68 ASN cc_start: 0.8058 (m-40) cc_final: 0.7827 (m-40) REVERT: C 95 LYS cc_start: 0.7242 (mtpt) cc_final: 0.6843 (mttm) REVERT: C 99 GLU cc_start: 0.5776 (mm-30) cc_final: 0.5481 (mm-30) REVERT: C 156 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: C 215 GLU cc_start: 0.7076 (pm20) cc_final: 0.6492 (pt0) REVERT: D 17 ASP cc_start: 0.8314 (m-30) cc_final: 0.8061 (m-30) REVERT: D 49 MET cc_start: 0.8463 (mtp) cc_final: 0.8198 (mtm) REVERT: D 99 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7733 (mtpt) REVERT: E 33 LYS cc_start: 0.8287 (mttt) cc_final: 0.7727 (mtmt) REVERT: E 51 ILE cc_start: 0.8327 (mm) cc_final: 0.8051 (mt) REVERT: E 92 GLN cc_start: 0.7445 (mt0) cc_final: 0.7009 (mt0) REVERT: E 197 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7398 (mp10) REVERT: F 80 ARG cc_start: 0.4439 (mtt-85) cc_final: 0.3858 (ptp90) REVERT: F 199 ARG cc_start: 0.6628 (ptt90) cc_final: 0.5180 (ptt180) REVERT: F 272 THR cc_start: 0.6360 (OUTLIER) cc_final: 0.6041 (p) REVERT: F 289 ARG cc_start: 0.5335 (ttt-90) cc_final: 0.4771 (tmt170) REVERT: F 309 TYR cc_start: 0.5771 (t80) cc_final: 0.4825 (t80) REVERT: F 317 MET cc_start: 0.6672 (mtt) cc_final: 0.6269 (mmt) outliers start: 46 outliers final: 22 residues processed: 231 average time/residue: 0.5733 time to fit residues: 145.0074 Evaluate side-chains 224 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 41 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 202 GLN F 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.184843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128883 restraints weight = 12387.102| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.56 r_work: 0.3053 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15088 Z= 0.182 Angle : 0.619 13.334 20478 Z= 0.322 Chirality : 0.046 0.259 2320 Planarity : 0.005 0.053 2567 Dihedral : 6.700 59.884 2223 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.11 % Allowed : 13.33 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.19), residues: 1882 helix: 1.36 (0.17), residues: 866 sheet: 0.61 (0.40), residues: 166 loop : -0.58 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 229 TYR 0.016 0.002 TYR D 141 PHE 0.022 0.002 PHE F 11 TRP 0.022 0.002 TRP B 103 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00428 (15081) covalent geometry : angle 0.61227 (20468) hydrogen bonds : bond 0.05893 ( 744) hydrogen bonds : angle 4.77546 ( 2103) metal coordination : bond 0.01123 ( 7) metal coordination : angle 4.26592 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6045 (ttp) cc_final: 0.5403 (mtp) REVERT: A 46 ARG cc_start: 0.7881 (ptp90) cc_final: 0.7383 (mtp180) REVERT: A 50 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8000 (mp0) REVERT: A 59 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 235 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7907 (t) REVERT: A 284 GLU cc_start: 0.7941 (tt0) cc_final: 0.6862 (mp0) REVERT: A 363 MET cc_start: 0.8802 (mtt) cc_final: 0.8564 (mtt) REVERT: A 384 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7312 (tmm) REVERT: A 433 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7972 (mm110) REVERT: B 144 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 380 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8441 (tp30) REVERT: B 406 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7482 (mtmt) REVERT: C 48 LYS cc_start: 0.7395 (mmmt) cc_final: 0.6900 (mttp) REVERT: C 68 ASN cc_start: 0.8049 (m-40) cc_final: 0.7803 (m-40) REVERT: C 95 LYS cc_start: 0.7271 (mtpt) cc_final: 0.6809 (mttm) REVERT: C 99 GLU cc_start: 0.5819 (mm-30) cc_final: 0.5565 (mm-30) REVERT: C 109 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7251 (tp30) REVERT: C 156 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: C 215 GLU cc_start: 0.7004 (pm20) cc_final: 0.6444 (pt0) REVERT: D 17 ASP cc_start: 0.8320 (m-30) cc_final: 0.8049 (m-30) REVERT: D 49 MET cc_start: 0.8484 (mtp) cc_final: 0.8206 (mtm) REVERT: D 99 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7783 (mtpt) REVERT: E 33 LYS cc_start: 0.8312 (mttt) cc_final: 0.7763 (mtmt) REVERT: E 51 ILE cc_start: 0.8336 (mm) cc_final: 0.8075 (mt) REVERT: E 92 GLN cc_start: 0.7508 (mt0) cc_final: 0.7069 (mt0) REVERT: E 197 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: F 80 ARG cc_start: 0.4585 (mtt-85) cc_final: 0.4021 (ptp90) REVERT: F 199 ARG cc_start: 0.6701 (ptt90) cc_final: 0.5253 (ppt170) REVERT: F 272 THR cc_start: 0.6190 (OUTLIER) cc_final: 0.5957 (p) REVERT: F 289 ARG cc_start: 0.5458 (ttt-90) cc_final: 0.4919 (tmt170) REVERT: F 291 HIS cc_start: 0.3870 (OUTLIER) cc_final: 0.3059 (m90) REVERT: F 309 TYR cc_start: 0.5825 (t80) cc_final: 0.5618 (t80) REVERT: F 317 MET cc_start: 0.6654 (mtt) cc_final: 0.6246 (mmt) outliers start: 48 outliers final: 23 residues processed: 228 average time/residue: 0.7294 time to fit residues: 180.8555 Evaluate side-chains 227 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 82 optimal weight: 0.0470 chunk 171 optimal weight: 40.0000 chunk 162 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 overall best weight: 1.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 202 GLN D 100 GLN F 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.185611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129134 restraints weight = 12289.681| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.59 r_work: 0.3078 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15088 Z= 0.154 Angle : 0.582 13.259 20478 Z= 0.304 Chirality : 0.045 0.233 2320 Planarity : 0.005 0.049 2567 Dihedral : 6.556 59.817 2223 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.04 % Allowed : 13.72 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.19), residues: 1882 helix: 1.39 (0.17), residues: 866 sheet: 0.58 (0.40), residues: 166 loop : -0.60 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 229 TYR 0.016 0.001 TYR D 141 PHE 0.019 0.002 PHE D 50 TRP 0.022 0.002 TRP B 103 HIS 0.020 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00353 (15081) covalent geometry : angle 0.57567 (20468) hydrogen bonds : bond 0.05410 ( 744) hydrogen bonds : angle 4.69766 ( 2103) metal coordination : bond 0.01081 ( 7) metal coordination : angle 4.00243 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6106 (ttp) cc_final: 0.5442 (mtp) REVERT: A 46 ARG cc_start: 0.7893 (ptp90) cc_final: 0.7402 (mtp180) REVERT: A 50 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8019 (mp0) REVERT: A 59 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8154 (mt-10) REVERT: A 259 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7329 (mt0) REVERT: A 284 GLU cc_start: 0.7946 (tt0) cc_final: 0.6862 (mp0) REVERT: A 363 MET cc_start: 0.8820 (mtt) cc_final: 0.8567 (mtt) REVERT: A 384 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7355 (tmm) REVERT: B 144 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8062 (mm-30) REVERT: B 380 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8416 (tp30) REVERT: B 406 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7578 (mtmt) REVERT: C 48 LYS cc_start: 0.7395 (mmmt) cc_final: 0.6888 (mttp) REVERT: C 68 ASN cc_start: 0.8001 (m-40) cc_final: 0.7754 (m-40) REVERT: C 95 LYS cc_start: 0.7254 (mtpt) cc_final: 0.6793 (mttm) REVERT: C 99 GLU cc_start: 0.5766 (mm-30) cc_final: 0.5480 (mm-30) REVERT: C 109 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: C 156 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7617 (mm-30) REVERT: C 215 GLU cc_start: 0.7004 (pm20) cc_final: 0.6431 (pt0) REVERT: D 17 ASP cc_start: 0.8319 (m-30) cc_final: 0.8042 (m-30) REVERT: D 49 MET cc_start: 0.8479 (mtp) cc_final: 0.8202 (mtm) REVERT: D 99 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7793 (mtpt) REVERT: E 33 LYS cc_start: 0.8331 (mttt) cc_final: 0.7785 (mtmt) REVERT: E 51 ILE cc_start: 0.8333 (mm) cc_final: 0.8085 (mt) REVERT: E 92 GLN cc_start: 0.7517 (mt0) cc_final: 0.7088 (mt0) REVERT: E 197 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: F 80 ARG cc_start: 0.4597 (mtt-85) cc_final: 0.4046 (ptp90) REVERT: F 272 THR cc_start: 0.6162 (OUTLIER) cc_final: 0.5930 (p) REVERT: F 289 ARG cc_start: 0.5361 (ttt-90) cc_final: 0.4841 (tmt170) REVERT: F 291 HIS cc_start: 0.3970 (OUTLIER) cc_final: 0.3209 (m90) REVERT: F 314 LYS cc_start: 0.5877 (OUTLIER) cc_final: 0.5448 (tptt) REVERT: F 317 MET cc_start: 0.6654 (mtt) cc_final: 0.6226 (mmt) REVERT: F 366 ASP cc_start: 0.7720 (m-30) cc_final: 0.7512 (m-30) outliers start: 47 outliers final: 27 residues processed: 221 average time/residue: 0.7222 time to fit residues: 174.0757 Evaluate side-chains 227 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 314 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 141 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 202 GLN A 433 GLN D 100 GLN F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.188726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.124731 restraints weight = 11799.983| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.03 r_work: 0.2989 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15088 Z= 0.140 Angle : 0.559 13.200 20478 Z= 0.293 Chirality : 0.044 0.233 2320 Planarity : 0.005 0.050 2567 Dihedral : 6.456 59.747 2223 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.11 % Allowed : 13.85 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.19), residues: 1882 helix: 1.48 (0.17), residues: 866 sheet: 0.61 (0.40), residues: 166 loop : -0.57 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 229 TYR 0.016 0.001 TYR D 141 PHE 0.019 0.002 PHE D 50 TRP 0.022 0.002 TRP B 103 HIS 0.018 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00314 (15081) covalent geometry : angle 0.55327 (20468) hydrogen bonds : bond 0.05127 ( 744) hydrogen bonds : angle 4.63459 ( 2103) metal coordination : bond 0.00868 ( 7) metal coordination : angle 3.80437 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6187 (ttp) cc_final: 0.5475 (mtp) REVERT: A 46 ARG cc_start: 0.7858 (ptp90) cc_final: 0.7333 (mtp180) REVERT: A 50 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8146 (mp0) REVERT: A 59 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 259 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: A 284 GLU cc_start: 0.7987 (tt0) cc_final: 0.6819 (mp0) REVERT: A 349 ARG cc_start: 0.8959 (mtm-85) cc_final: 0.8723 (mtm-85) REVERT: A 363 MET cc_start: 0.8854 (mtt) cc_final: 0.8600 (mtt) REVERT: A 433 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7945 (mm110) REVERT: B 325 MET cc_start: 0.8908 (ttm) cc_final: 0.8687 (ttp) REVERT: B 380 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: B 406 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7623 (mtmt) REVERT: C 48 LYS cc_start: 0.7310 (mmmt) cc_final: 0.6782 (mttp) REVERT: C 68 ASN cc_start: 0.7952 (m-40) cc_final: 0.7719 (m-40) REVERT: C 95 LYS cc_start: 0.7237 (mtpt) cc_final: 0.6791 (mttm) REVERT: C 99 GLU cc_start: 0.5591 (mm-30) cc_final: 0.5354 (mm-30) REVERT: C 109 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: C 156 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: C 215 GLU cc_start: 0.7054 (pm20) cc_final: 0.6381 (pt0) REVERT: D 17 ASP cc_start: 0.8318 (m-30) cc_final: 0.8056 (m-30) REVERT: D 49 MET cc_start: 0.8489 (mtp) cc_final: 0.8212 (mtm) REVERT: D 99 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7809 (mtpt) REVERT: E 33 LYS cc_start: 0.8323 (mttt) cc_final: 0.7796 (mtmt) REVERT: E 51 ILE cc_start: 0.8362 (mm) cc_final: 0.8114 (mt) REVERT: E 92 GLN cc_start: 0.7561 (mt0) cc_final: 0.7117 (mt0) REVERT: E 197 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: F 80 ARG cc_start: 0.4611 (mtt-85) cc_final: 0.4018 (ptp90) REVERT: F 135 CYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5450 (p) REVERT: F 272 THR cc_start: 0.6078 (OUTLIER) cc_final: 0.5845 (p) REVERT: F 289 ARG cc_start: 0.5308 (ttt-90) cc_final: 0.4877 (tmt170) REVERT: F 291 HIS cc_start: 0.3966 (OUTLIER) cc_final: 0.3274 (m90) REVERT: F 309 TYR cc_start: 0.5611 (t80) cc_final: 0.4779 (t80) REVERT: F 317 MET cc_start: 0.6619 (mtt) cc_final: 0.6205 (mmt) REVERT: F 366 ASP cc_start: 0.7682 (m-30) cc_final: 0.7474 (m-30) outliers start: 48 outliers final: 26 residues processed: 223 average time/residue: 0.7288 time to fit residues: 177.6043 Evaluate side-chains 229 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 135 CYS Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 202 GLN D 100 GLN F 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.188283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.169200 restraints weight = 11851.076| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 0.66 r_work: 0.3654 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15088 Z= 0.154 Angle : 0.579 13.123 20478 Z= 0.302 Chirality : 0.044 0.234 2320 Planarity : 0.005 0.053 2567 Dihedral : 6.545 59.846 2223 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.17 % Allowed : 13.85 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.19), residues: 1882 helix: 1.43 (0.17), residues: 866 sheet: 0.61 (0.40), residues: 166 loop : -0.58 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 229 TYR 0.016 0.001 TYR D 141 PHE 0.019 0.002 PHE D 50 TRP 0.022 0.002 TRP B 103 HIS 0.014 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00354 (15081) covalent geometry : angle 0.57345 (20468) hydrogen bonds : bond 0.05333 ( 744) hydrogen bonds : angle 4.65671 ( 2103) metal coordination : bond 0.00944 ( 7) metal coordination : angle 3.77463 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6427 (ttp) cc_final: 0.6089 (mtp) REVERT: A 363 MET cc_start: 0.8666 (mtt) cc_final: 0.8378 (mtt) REVERT: A 384 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7405 (tmm) REVERT: B 380 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8313 (tp30) REVERT: B 406 LYS cc_start: 0.8401 (ttmm) cc_final: 0.7933 (mtmt) REVERT: D 17 ASP cc_start: 0.8511 (m-30) cc_final: 0.8258 (m-30) REVERT: D 49 MET cc_start: 0.8519 (mtp) cc_final: 0.8289 (mtm) REVERT: E 33 LYS cc_start: 0.8398 (mttt) cc_final: 0.8164 (mtmt) REVERT: E 51 ILE cc_start: 0.8452 (mm) cc_final: 0.8229 (mt) REVERT: E 92 GLN cc_start: 0.8402 (mt0) cc_final: 0.8177 (mt0) REVERT: F 291 HIS cc_start: 0.5175 (OUTLIER) cc_final: 0.4687 (m90) outliers start: 49 outliers final: 27 residues processed: 222 average time/residue: 0.7135 time to fit residues: 172.7833 Evaluate side-chains 213 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 146 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 141 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 202 GLN A 433 GLN C 68 ASN D 100 GLN F 291 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.186572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.165617 restraints weight = 11978.751| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 0.71 r_work: 0.3167 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15088 Z= 0.187 Angle : 0.630 13.087 20478 Z= 0.326 Chirality : 0.046 0.252 2320 Planarity : 0.005 0.057 2567 Dihedral : 6.807 59.871 2223 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.46 % Allowed : 15.34 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.19), residues: 1882 helix: 1.29 (0.17), residues: 867 sheet: 0.64 (0.39), residues: 165 loop : -0.60 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 229 TYR 0.016 0.002 TYR D 141 PHE 0.022 0.002 PHE F 11 TRP 0.021 0.002 TRP B 103 HIS 0.021 0.002 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00442 (15081) covalent geometry : angle 0.62419 (20468) hydrogen bonds : bond 0.05849 ( 744) hydrogen bonds : angle 4.74106 ( 2103) metal coordination : bond 0.01154 ( 7) metal coordination : angle 3.97415 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6292 (ttp) cc_final: 0.5737 (mtp) REVERT: A 349 ARG cc_start: 0.8935 (mtm-85) cc_final: 0.8664 (mtm-85) REVERT: A 363 MET cc_start: 0.8856 (mtt) cc_final: 0.8610 (mtt) REVERT: A 384 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7427 (tmm) REVERT: B 380 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8415 (tp30) REVERT: B 406 LYS cc_start: 0.8504 (ttmm) cc_final: 0.7799 (mtmt) REVERT: D 49 MET cc_start: 0.8602 (mtp) cc_final: 0.8341 (mtm) REVERT: E 33 LYS cc_start: 0.8470 (mttt) cc_final: 0.8018 (mtmt) REVERT: E 51 ILE cc_start: 0.8489 (mm) cc_final: 0.8238 (mt) REVERT: E 92 GLN cc_start: 0.7961 (mt0) cc_final: 0.7547 (mt0) REVERT: F 291 HIS cc_start: 0.4171 (OUTLIER) cc_final: 0.3817 (m90) outliers start: 38 outliers final: 27 residues processed: 198 average time/residue: 0.6513 time to fit residues: 141.3682 Evaluate side-chains 209 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 43 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 chunk 179 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 180 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 202 GLN A 433 GLN D 100 GLN F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.189917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.127366 restraints weight = 11899.950| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.03 r_work: 0.2990 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15088 Z= 0.114 Angle : 0.532 13.039 20478 Z= 0.280 Chirality : 0.042 0.234 2320 Planarity : 0.005 0.057 2567 Dihedral : 6.458 59.584 2223 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.62 % Allowed : 15.99 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.19), residues: 1882 helix: 1.63 (0.18), residues: 867 sheet: 0.56 (0.39), residues: 168 loop : -0.54 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 229 TYR 0.016 0.001 TYR D 141 PHE 0.018 0.001 PHE D 50 TRP 0.020 0.001 TRP B 103 HIS 0.027 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00244 (15081) covalent geometry : angle 0.52701 (20468) hydrogen bonds : bond 0.04535 ( 744) hydrogen bonds : angle 4.52189 ( 2103) metal coordination : bond 0.00658 ( 7) metal coordination : angle 3.45240 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6208 (ttp) cc_final: 0.5474 (mtp) REVERT: A 349 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8522 (mtm-85) REVERT: A 363 MET cc_start: 0.8847 (mtt) cc_final: 0.8578 (mtt) REVERT: A 384 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7277 (tmm) REVERT: B 380 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8320 (tp30) REVERT: B 406 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7549 (mtmt) REVERT: D 17 ASP cc_start: 0.8316 (m-30) cc_final: 0.8045 (m-30) REVERT: D 49 MET cc_start: 0.8442 (mtp) cc_final: 0.8168 (mtm) REVERT: E 33 LYS cc_start: 0.8317 (mttt) cc_final: 0.7793 (mtmt) REVERT: E 92 GLN cc_start: 0.7544 (mt0) cc_final: 0.7081 (mt0) REVERT: E 109 LEU cc_start: 0.3800 (OUTLIER) cc_final: 0.3279 (pp) REVERT: F 405 ASP cc_start: 0.5655 (t0) cc_final: 0.5431 (p0) outliers start: 25 outliers final: 16 residues processed: 207 average time/residue: 0.7063 time to fit residues: 160.3833 Evaluate side-chains 202 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 245 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 94 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 170 optimal weight: 50.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 202 GLN A 433 GLN B 330 HIS C 68 ASN D 100 GLN F 291 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.185682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.127911 restraints weight = 11863.743| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.26 r_work: 0.2989 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15088 Z= 0.236 Angle : 0.694 13.033 20478 Z= 0.359 Chirality : 0.050 0.305 2320 Planarity : 0.006 0.060 2567 Dihedral : 7.236 59.941 2223 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.14 % Allowed : 15.86 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.18), residues: 1882 helix: 1.16 (0.17), residues: 868 sheet: 0.64 (0.39), residues: 165 loop : -0.64 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 229 TYR 0.018 0.002 TYR B 412 PHE 0.025 0.003 PHE F 11 TRP 0.020 0.003 TRP B 70 HIS 0.007 0.002 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00570 (15081) covalent geometry : angle 0.68820 (20468) hydrogen bonds : bond 0.06550 ( 744) hydrogen bonds : angle 4.85150 ( 2103) metal coordination : bond 0.01413 ( 7) metal coordination : angle 3.99107 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6040.51 seconds wall clock time: 103 minutes 32.86 seconds (6212.86 seconds total)