Starting phenix.real_space_refine on Fri Jul 3 14:56:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ud6_64063/07_2026/9ud6_64063.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ud6_64063/07_2026/9ud6_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_64063/07_2026/9ud6_64063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ud6_64063/07_2026/9ud6_64063.map" model { file = "/net/cci-nas-00/data/ceres_data/9ud6_64063/07_2026/9ud6_64063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ud6_64063/07_2026/9ud6_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-dev-6108/lib/python3.11/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, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 2.68, per 1000 atoms: 0.18 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: 1.22 Conformation dependent library (CDL) restraints added in 528.9 milliseconds 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: 0.34 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: 2.12 Time building geometry restraints manager: 1.58 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: 1.970 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 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 are 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/Z covalent geometry : bond 0.00379 / 0.17 (15081) covalent geometry : angle 0.55813 / 0.30 (20468) hydrogen bonds : bond 0.12519 / 8.56 ( 744) hydrogen bonds : angle 5.51000 / 3.83 ( 2103) metal coordination : bond 0.33469 / 13.39 ( 7) metal coordination : angle 10.74966 / 7.29 ( 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 : 0.362 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: 0.5784 time to fit residues: 193.4617 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 : 0.544 ------------------------------------------------------------------------------- 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... 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 = 0.3969 r_free = 0.3969 target = 0.184942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128712 restraints weight = 12295.432| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.56 r_work: 0.3063 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 13.588 20478 Z= 0.341 Chirality : 0.048 0.251 2320 Planarity : 0.005 0.058 2567 Dihedral : 6.872 74.684 2228 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.54 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 are 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/Z covalent geometry : bond 0.00454 / 0.19 (15081) covalent geometry : angle 0.64699 / 0.34 (20468) hydrogen bonds : bond 0.06067 / 3.98 ( 744) hydrogen bonds : angle 4.92058 / 3.41 ( 2103) metal coordination : bond 0.01467 / 0.84 ( 7) metal coordination : angle 7.69917 / 4.87 ( 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 : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6059 (ttp) cc_final: 0.5453 (mtp) REVERT: A 46 ARG cc_start: 0.7808 (ptp90) cc_final: 0.7452 (mtp-110) REVERT: A 50 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8099 (tp30) REVERT: A 59 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8018 (mt-10) REVERT: A 62 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7585 (mtmt) REVERT: A 235 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7964 (t) REVERT: A 284 GLU cc_start: 0.7925 (tt0) cc_final: 0.6924 (mp0) REVERT: A 363 MET cc_start: 0.8807 (mtt) cc_final: 0.8565 (mtt) REVERT: B 43 ARG cc_start: 0.6956 (tpp80) cc_final: 0.6637 (tpp-160) REVERT: B 144 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8054 (mm-30) REVERT: B 380 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8415 (tp30) REVERT: B 406 LYS cc_start: 0.8363 (ttmm) cc_final: 0.7521 (mtmt) REVERT: C 48 LYS cc_start: 0.7410 (mmmt) cc_final: 0.6830 (mttp) REVERT: C 68 ASN cc_start: 0.8062 (m-40) cc_final: 0.7797 (m-40) REVERT: C 85 GLU cc_start: 0.7491 (mp0) cc_final: 0.7257 (mp0) REVERT: C 95 LYS cc_start: 0.7209 (mtpt) cc_final: 0.6848 (mttm) REVERT: C 99 GLU cc_start: 0.5525 (mm-30) cc_final: 0.5279 (mm-30) REVERT: C 109 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: C 156 GLU cc_start: 0.8097 (tp30) cc_final: 0.7658 (mm-30) REVERT: C 165 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8376 (tt) REVERT: C 215 GLU cc_start: 0.6985 (pm20) cc_final: 0.6439 (pt0) REVERT: D 17 ASP cc_start: 0.8340 (m-30) cc_final: 0.8076 (m-30) REVERT: D 49 MET cc_start: 0.8492 (mtp) cc_final: 0.8229 (mtm) REVERT: D 99 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7782 (mtpt) REVERT: D 207 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8017 (mt-10) REVERT: E 33 LYS cc_start: 0.8276 (mttt) cc_final: 0.7732 (mtmt) REVERT: E 51 ILE cc_start: 0.8360 (mm) cc_final: 0.8073 (mt) REVERT: E 92 GLN cc_start: 0.7445 (mt0) cc_final: 0.7040 (mt0) REVERT: E 197 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: F 80 ARG cc_start: 0.4401 (mtt-85) cc_final: 0.3657 (ptp90) REVERT: F 199 ARG cc_start: 0.6318 (ptt-90) cc_final: 0.6060 (ptt90) REVERT: F 289 ARG cc_start: 0.5418 (ttt-90) cc_final: 0.4839 (tmt170) REVERT: F 309 TYR cc_start: 0.5737 (t80) cc_final: 0.5521 (t80) REVERT: F 317 MET cc_start: 0.6784 (mtt) cc_final: 0.6449 (mmt) outliers start: 46 outliers final: 20 residues processed: 252 average time/residue: 0.5663 time to fit residues: 156.3000 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 : 0.530 ------------------------------------------------------------------------------- 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: 0.0020 chunk 127 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3994 r_free = 0.3994 target = 0.187706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.132290 restraints weight = 12476.220| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.59 r_work: 0.3100 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15088 Z= 0.119 Angle : 0.535 13.522 20478 Z= 0.278 Chirality : 0.043 0.231 2320 Planarity : 0.004 0.040 2567 Dihedral : 6.250 66.643 2224 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.59 % Allowed : 12.17 % Favored : 85.24 % 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 are not related in a simple way. whole: 0.99 (0.19), residues: 1882 helix: 1.71 (0.18), residues: 864 sheet: 0.62 (0.40), residues: 166 loop : -0.40 (0.20), residues: 852 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 0.001 TRP B 103 HIS 0.004 0.001 HIS E 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (15081) covalent geometry : angle 0.52212 / 0.28 (20468) hydrogen bonds : bond 0.04645 / 3.06 ( 744) hydrogen bonds : angle 4.62697 / 3.20 ( 2103) metal coordination : bond 0.01239 / 0.60 ( 7) metal coordination : angle 5.29277 / 3.33 ( 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 249 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6017 (ttp) cc_final: 0.5415 (mtp) REVERT: A 46 ARG cc_start: 0.7782 (ptp90) cc_final: 0.7318 (mtp180) REVERT: A 50 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8054 (mp0) REVERT: A 59 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 200 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.7803 (mtp180) REVERT: A 363 MET cc_start: 0.8837 (mtt) cc_final: 0.8579 (mtt) REVERT: B 380 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8301 (tp30) REVERT: B 406 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7602 (mtmt) REVERT: C 45 LYS cc_start: 0.6960 (ttpt) cc_final: 0.6427 (tppt) REVERT: C 48 LYS cc_start: 0.7385 (mmmt) cc_final: 0.6858 (mttm) REVERT: C 68 ASN cc_start: 0.8062 (m-40) cc_final: 0.7833 (m-40) REVERT: C 85 GLU cc_start: 0.7512 (mp0) cc_final: 0.7220 (mp0) REVERT: C 95 LYS cc_start: 0.7173 (mtpt) cc_final: 0.6810 (mttm) REVERT: C 99 GLU cc_start: 0.5649 (mm-30) cc_final: 0.5338 (mm-30) REVERT: C 156 GLU cc_start: 0.7999 (tp30) cc_final: 0.7653 (mm-30) REVERT: C 215 GLU cc_start: 0.7049 (pm20) cc_final: 0.6468 (pt0) REVERT: D 17 ASP cc_start: 0.8328 (m-30) cc_final: 0.8031 (m-30) REVERT: D 49 MET cc_start: 0.8413 (mtp) cc_final: 0.8145 (mtm) REVERT: D 99 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7754 (mtpt) REVERT: D 207 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8025 (mt-10) REVERT: E 33 LYS cc_start: 0.8260 (mttt) cc_final: 0.7704 (mtmt) REVERT: E 51 ILE cc_start: 0.8316 (mm) cc_final: 0.8026 (mt) REVERT: E 92 GLN cc_start: 0.7408 (mt0) cc_final: 0.6968 (mt0) REVERT: E 190 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7794 (t80) REVERT: E 197 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: F 80 ARG cc_start: 0.4344 (mtt-85) cc_final: 0.3694 (ptp90) REVERT: F 288 MET cc_start: 0.4767 (mmp) cc_final: 0.4545 (mmp) REVERT: F 289 ARG cc_start: 0.5336 (ttt-90) cc_final: 0.4797 (ttt-90) REVERT: F 303 ARG cc_start: 0.4697 (mtp180) cc_final: 0.4328 (mtp180) REVERT: F 317 MET cc_start: 0.6626 (mtt) cc_final: 0.6265 (mmt) outliers start: 40 outliers final: 14 residues processed: 235 average time/residue: 0.5748 time to fit residues: 147.6808 Evaluate side-chains 218 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 1 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 176 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3992 r_free = 0.3992 target = 0.187508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131964 restraints weight = 12402.782| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.59 r_work: 0.3092 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1678 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= 0.126 Angle : 0.541 13.452 20478 Z= 0.282 Chirality : 0.043 0.230 2320 Planarity : 0.005 0.045 2567 Dihedral : 6.248 59.712 2223 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.24 % Allowed : 12.43 % Favored : 84.34 % 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 are not related in a simple way. whole: 0.99 (0.19), residues: 1882 helix: 1.71 (0.18), residues: 863 sheet: 0.60 (0.40), residues: 168 loop : -0.40 (0.20), residues: 851 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 0.001 PHE D 50 TRP 0.021 0.002 TRP B 103 HIS 0.004 0.001 HIS E 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (15081) covalent geometry : angle 0.53292 / 0.28 (20468) hydrogen bonds : bond 0.04745 / 3.11 ( 744) hydrogen bonds : angle 4.57000 / 3.17 ( 2103) metal coordination : bond 0.01074 / 0.49 ( 7) metal coordination : angle 4.32896 / 2.59 ( 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 254 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.501 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: 0.6024 (ttp) cc_final: 0.5417 (mtp) REVERT: A 46 ARG cc_start: 0.7858 (ptp90) cc_final: 0.7400 (mtp180) REVERT: A 50 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8053 (mp0) REVERT: A 59 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8002 (mt-10) REVERT: A 284 GLU cc_start: 0.7939 (tt0) cc_final: 0.6837 (mp0) REVERT: A 349 ARG cc_start: 0.8782 (mtm-85) cc_final: 0.8547 (mtm-85) REVERT: A 363 MET cc_start: 0.8815 (mtt) cc_final: 0.8541 (mtt) REVERT: A 384 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7222 (tmm) REVERT: A 433 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7895 (mm110) REVERT: B 380 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8304 (tp30) REVERT: B 406 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7543 (mtmt) REVERT: C 45 LYS cc_start: 0.7040 (ttpt) cc_final: 0.6478 (tppt) REVERT: C 48 LYS cc_start: 0.7386 (mmmt) cc_final: 0.6859 (mttm) REVERT: C 68 ASN cc_start: 0.8017 (m-40) cc_final: 0.7787 (m-40) REVERT: C 95 LYS cc_start: 0.7261 (mtpt) cc_final: 0.6883 (mttm) REVERT: C 99 GLU cc_start: 0.5733 (mm-30) cc_final: 0.5453 (mm-30) REVERT: C 156 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: C 165 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8327 (tt) REVERT: C 215 GLU cc_start: 0.7054 (pm20) cc_final: 0.6484 (pt0) REVERT: D 17 ASP cc_start: 0.8341 (m-30) cc_final: 0.8052 (m-30) REVERT: D 49 MET cc_start: 0.8420 (mtp) cc_final: 0.8154 (mtm) REVERT: D 99 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7726 (mtpt) REVERT: E 33 LYS cc_start: 0.8290 (mttt) cc_final: 0.7746 (mtmt) REVERT: E 51 ILE cc_start: 0.8316 (mm) cc_final: 0.8032 (mt) REVERT: E 92 GLN cc_start: 0.7430 (mt0) cc_final: 0.7009 (mt0) REVERT: E 190 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7823 (t80) REVERT: E 197 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: F 80 ARG cc_start: 0.4414 (mtt-85) cc_final: 0.3830 (ptp90) REVERT: F 199 ARG cc_start: 0.6669 (ptt90) cc_final: 0.5157 (ptt180) REVERT: F 272 THR cc_start: 0.6399 (OUTLIER) cc_final: 0.6074 (p) REVERT: F 289 ARG cc_start: 0.5348 (ttt-90) cc_final: 0.4837 (ttt-90) REVERT: F 309 TYR cc_start: 0.5779 (t80) cc_final: 0.4909 (t80) REVERT: F 317 MET cc_start: 0.6660 (mtt) cc_final: 0.6274 (mmt) REVERT: F 366 ASP cc_start: 0.7705 (m-30) cc_final: 0.7472 (m-30) outliers start: 50 outliers final: 21 residues processed: 235 average time/residue: 0.5602 time to fit residues: 143.9627 Evaluate side-chains 228 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 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 109 LEU 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 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: 10.0000 chunk 135 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3966 r_free = 0.3966 target = 0.184806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128616 restraints weight = 12361.389| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.62 r_work: 0.3054 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15088 Z= 0.191 Angle : 0.628 13.347 20478 Z= 0.327 Chirality : 0.047 0.265 2320 Planarity : 0.005 0.055 2567 Dihedral : 6.754 59.747 2223 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.91 % Allowed : 13.40 % Favored : 83.69 % 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 are not related in a simple way. whole: 0.63 (0.19), residues: 1882 helix: 1.35 (0.17), residues: 866 sheet: 0.60 (0.40), residues: 166 loop : -0.56 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 229 TYR 0.016 0.002 TYR D 141 PHE 0.023 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/Z covalent geometry : bond 0.00453 / 0.19 (15081) covalent geometry : angle 0.62104 / 0.33 (20468) hydrogen bonds : bond 0.06011 / 3.93 ( 744) hydrogen bonds : angle 4.78903 / 3.32 ( 2103) metal coordination : bond 0.01161 / 0.59 ( 7) metal coordination : angle 4.33649 / 2.53 ( 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 247 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6061 (ttp) cc_final: 0.5425 (mtp) REVERT: A 46 ARG cc_start: 0.7894 (ptp90) cc_final: 0.7406 (mtp180) REVERT: A 50 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8025 (mp0) REVERT: A 59 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 284 GLU cc_start: 0.7967 (tt0) cc_final: 0.6894 (mp0) REVERT: A 363 MET cc_start: 0.8812 (mtt) cc_final: 0.8577 (mtt) REVERT: A 384 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7308 (tmm) REVERT: A 433 GLN cc_start: 0.8241 (mm-40) cc_final: 0.8007 (mm110) REVERT: B 42 LYS cc_start: 0.8023 (mtmp) cc_final: 0.7775 (mtmt) REVERT: B 144 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8091 (mm-30) REVERT: B 380 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8454 (tp30) REVERT: B 406 LYS cc_start: 0.8307 (ttmm) cc_final: 0.7503 (mtmt) REVERT: C 48 LYS cc_start: 0.7421 (mmmt) cc_final: 0.6932 (mttp) REVERT: C 68 ASN cc_start: 0.8051 (m-40) cc_final: 0.7806 (m-40) REVERT: C 95 LYS cc_start: 0.7284 (mtpt) cc_final: 0.6834 (mttm) REVERT: C 99 GLU cc_start: 0.5791 (mm-30) cc_final: 0.5527 (mm-30) REVERT: C 109 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: C 156 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: C 215 GLU cc_start: 0.7008 (pm20) cc_final: 0.6452 (pt0) REVERT: D 17 ASP cc_start: 0.8367 (m-30) cc_final: 0.8102 (m-30) REVERT: D 49 MET cc_start: 0.8499 (mtp) cc_final: 0.8221 (mtm) REVERT: D 99 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7806 (mtpt) REVERT: E 33 LYS cc_start: 0.8327 (mttt) cc_final: 0.7775 (mtmt) REVERT: E 51 ILE cc_start: 0.8356 (mm) cc_final: 0.8098 (mt) REVERT: E 92 GLN cc_start: 0.7508 (mt0) cc_final: 0.7069 (mt0) REVERT: E 197 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: F 80 ARG cc_start: 0.4588 (mtt-85) cc_final: 0.4020 (ptp90) REVERT: F 199 ARG cc_start: 0.6704 (ptt90) cc_final: 0.5259 (ppt170) REVERT: F 272 THR cc_start: 0.6199 (OUTLIER) cc_final: 0.5963 (p) REVERT: F 289 ARG cc_start: 0.5493 (ttt-90) cc_final: 0.4963 (tmt170) REVERT: F 291 HIS cc_start: 0.3981 (OUTLIER) cc_final: 0.3159 (m90) REVERT: F 309 TYR cc_start: 0.5888 (t80) cc_final: 0.5067 (t80) REVERT: F 317 MET cc_start: 0.6632 (mtt) cc_final: 0.6212 (mmt) REVERT: F 346 ASP cc_start: 0.4215 (m-30) cc_final: 0.3735 (m-30) outliers start: 45 outliers final: 23 residues processed: 227 average time/residue: 0.6045 time to fit residues: 150.0233 Evaluate side-chains 228 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 52 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 122 optimal weight: 0.0670 chunk 120 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 82 optimal weight: 0.0070 chunk 171 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 202 GLN B 330 HIS 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 = 0.3969 r_free = 0.3969 target = 0.185177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.130215 restraints weight = 12288.053| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.61 r_work: 0.3055 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1917 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= 0.171 Angle : 0.603 13.261 20478 Z= 0.315 Chirality : 0.046 0.238 2320 Planarity : 0.005 0.051 2567 Dihedral : 6.662 59.759 2223 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.24 % Allowed : 13.59 % Favored : 83.17 % 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 are not related in a simple way. whole: 0.59 (0.19), residues: 1882 helix: 1.32 (0.17), residues: 866 sheet: 0.58 (0.40), residues: 166 loop : -0.59 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 229 TYR 0.016 0.002 TYR D 141 PHE 0.020 0.002 PHE F 11 TRP 0.021 0.002 TRP B 103 HIS 0.008 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (15081) covalent geometry : angle 0.59652 / 0.31 (20468) hydrogen bonds : bond 0.05681 / 3.71 ( 744) hydrogen bonds : angle 4.74314 / 3.29 ( 2103) metal coordination : bond 0.01134 / 0.55 ( 7) metal coordination : angle 4.09629 / 2.39 ( 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 246 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6091 (ttp) cc_final: 0.5422 (mtp) REVERT: A 46 ARG cc_start: 0.7897 (ptp90) cc_final: 0.7403 (mtp180) REVERT: A 50 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8030 (mp0) REVERT: A 59 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8190 (mt-10) REVERT: A 235 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7943 (t) REVERT: A 259 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: A 284 GLU cc_start: 0.7963 (tt0) cc_final: 0.6904 (mp0) REVERT: A 349 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8585 (mtm-85) REVERT: A 363 MET cc_start: 0.8819 (mtt) cc_final: 0.8568 (mtt) REVERT: A 384 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7347 (tmm) REVERT: A 433 GLN cc_start: 0.8245 (mm-40) cc_final: 0.8003 (mm110) REVERT: B 42 LYS cc_start: 0.8006 (mtmp) cc_final: 0.7770 (mtmt) REVERT: B 144 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8092 (mm-30) REVERT: B 380 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8454 (tp30) REVERT: B 406 LYS cc_start: 0.8322 (ttmm) cc_final: 0.7531 (mtmt) REVERT: C 48 LYS cc_start: 0.7442 (mmmt) cc_final: 0.6946 (mttp) REVERT: C 68 ASN cc_start: 0.8061 (m-40) cc_final: 0.7822 (m-40) REVERT: C 95 LYS cc_start: 0.7290 (mtpt) cc_final: 0.6823 (mttm) REVERT: C 99 GLU cc_start: 0.5810 (mm-30) cc_final: 0.5522 (mm-30) REVERT: C 109 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: C 156 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: C 215 GLU cc_start: 0.7019 (pm20) cc_final: 0.6453 (pt0) REVERT: D 17 ASP cc_start: 0.8343 (m-30) cc_final: 0.8066 (m-30) REVERT: D 49 MET cc_start: 0.8508 (mtp) cc_final: 0.8228 (mtm) REVERT: D 99 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7826 (mtpt) REVERT: E 33 LYS cc_start: 0.8344 (mttt) cc_final: 0.7804 (mtmt) REVERT: E 51 ILE cc_start: 0.8352 (mm) cc_final: 0.8082 (mt) REVERT: E 92 GLN cc_start: 0.7558 (mt0) cc_final: 0.7138 (mt0) REVERT: E 197 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: F 80 ARG cc_start: 0.4571 (mtt-85) cc_final: 0.4024 (ptp90) REVERT: F 272 THR cc_start: 0.6125 (OUTLIER) cc_final: 0.5910 (p) REVERT: F 289 ARG cc_start: 0.5421 (ttt-90) cc_final: 0.4978 (tmt170) REVERT: F 291 HIS cc_start: 0.4374 (OUTLIER) cc_final: 0.3663 (m90) REVERT: F 309 TYR cc_start: 0.5894 (t80) cc_final: 0.5009 (t80) REVERT: F 317 MET cc_start: 0.6630 (mtt) cc_final: 0.6227 (mmt) outliers start: 50 outliers final: 26 residues processed: 225 average time/residue: 0.6119 time to fit residues: 150.7702 Evaluate side-chains 229 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 235 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 141 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3964 r_free = 0.3964 target = 0.184594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.128490 restraints weight = 12289.033| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.60 r_work: 0.3055 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15088 Z= 0.191 Angle : 0.626 13.206 20478 Z= 0.326 Chirality : 0.047 0.258 2320 Planarity : 0.005 0.054 2567 Dihedral : 6.782 59.877 2223 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.17 % Allowed : 13.79 % 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 are not related in a simple way. whole: 0.50 (0.18), residues: 1882 helix: 1.24 (0.17), residues: 867 sheet: 0.56 (0.40), residues: 166 loop : -0.63 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 229 TYR 0.016 0.002 TYR D 141 PHE 0.022 0.002 PHE F 11 TRP 0.020 0.002 TRP B 103 HIS 0.009 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (15081) covalent geometry : angle 0.61986 / 0.33 (20468) hydrogen bonds : bond 0.05957 / 3.89 ( 744) hydrogen bonds : angle 4.78708 / 3.32 ( 2103) metal coordination : bond 0.01203 / 0.60 ( 7) metal coordination : angle 4.08270 / 2.36 ( 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 244 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.427 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: 0.6080 (ttp) cc_final: 0.5412 (mtp) REVERT: A 46 ARG cc_start: 0.7890 (ptp90) cc_final: 0.7401 (mtp180) REVERT: A 50 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7997 (mp0) REVERT: A 59 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8190 (mt-10) REVERT: A 235 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7929 (t) REVERT: A 284 GLU cc_start: 0.7949 (tt0) cc_final: 0.6842 (mp0) REVERT: A 349 ARG cc_start: 0.8816 (mtm-85) cc_final: 0.8485 (mtm-85) REVERT: A 363 MET cc_start: 0.8817 (mtt) cc_final: 0.8572 (mtt) REVERT: A 384 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.7346 (tmm) REVERT: A 433 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7971 (mm110) REVERT: B 42 LYS cc_start: 0.8035 (mtmp) cc_final: 0.7800 (mtmt) REVERT: B 144 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 380 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8454 (tp30) REVERT: B 406 LYS cc_start: 0.8320 (ttmm) cc_final: 0.7524 (mtmt) REVERT: C 48 LYS cc_start: 0.7448 (mmmt) cc_final: 0.6952 (mttp) REVERT: C 68 ASN cc_start: 0.8069 (m-40) cc_final: 0.7860 (m-40) REVERT: C 95 LYS cc_start: 0.7306 (mtpt) cc_final: 0.6819 (mttm) REVERT: C 99 GLU cc_start: 0.5761 (mm-30) cc_final: 0.5526 (mm-30) REVERT: C 109 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: C 156 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: C 215 GLU cc_start: 0.7020 (pm20) cc_final: 0.6465 (pt0) REVERT: D 17 ASP cc_start: 0.8338 (m-30) cc_final: 0.8056 (m-30) REVERT: D 49 MET cc_start: 0.8505 (mtp) cc_final: 0.8225 (mtm) REVERT: D 99 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7802 (mtpt) REVERT: E 33 LYS cc_start: 0.8316 (mttt) cc_final: 0.7779 (mtmt) REVERT: E 51 ILE cc_start: 0.8366 (mm) cc_final: 0.8097 (mt) REVERT: E 92 GLN cc_start: 0.7548 (mt0) cc_final: 0.7115 (mt0) REVERT: E 197 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7445 (mp10) REVERT: F 80 ARG cc_start: 0.4603 (mtt-85) cc_final: 0.4031 (ptp90) REVERT: F 272 THR cc_start: 0.6132 (OUTLIER) cc_final: 0.5924 (p) REVERT: F 289 ARG cc_start: 0.5438 (ttt-90) cc_final: 0.5061 (ttt-90) REVERT: F 309 TYR cc_start: 0.5781 (t80) cc_final: 0.4888 (t80) REVERT: F 314 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5434 (tptt) REVERT: F 317 MET cc_start: 0.6667 (mtt) cc_final: 0.6321 (mmt) outliers start: 49 outliers final: 26 residues processed: 224 average time/residue: 0.6206 time to fit residues: 151.7502 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 : 0.444 ------------------------------------------------------------------------------- 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 235 VAL 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 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 272 THR Chi-restraints excluded: chain F residue 314 LYS 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: 1.9990 chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 117 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4007 r_free = 0.4007 target = 0.188629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.167372 restraints weight = 11875.405| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 0.73 r_work: 0.3183 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2007 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= 0.143 Angle : 0.567 13.095 20478 Z= 0.297 Chirality : 0.044 0.235 2320 Planarity : 0.005 0.049 2567 Dihedral : 6.599 59.788 2223 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.46 % Allowed : 14.76 % Favored : 82.78 % 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 are not related in a simple way. whole: 0.67 (0.19), residues: 1882 helix: 1.44 (0.17), residues: 866 sheet: 0.59 (0.40), residues: 166 loop : -0.61 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 229 TYR 0.017 0.001 TYR D 141 PHE 0.019 0.002 PHE D 50 TRP 0.020 0.002 TRP B 103 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15081) covalent geometry : angle 0.56092 / 0.30 (20468) hydrogen bonds : bond 0.05147 / 3.37 ( 744) hydrogen bonds : angle 4.64770 / 3.22 ( 2103) metal coordination : bond 0.00893 / 0.44 ( 7) metal coordination : angle 3.66981 / 2.12 ( 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 237 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.391 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: 0.6277 (ttp) cc_final: 0.5740 (mtp) REVERT: A 46 ARG cc_start: 0.7981 (ptp90) cc_final: 0.7587 (mtp180) REVERT: A 50 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8134 (mp0) REVERT: A 59 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 235 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8102 (t) REVERT: A 284 GLU cc_start: 0.7976 (tt0) cc_final: 0.7134 (mp0) REVERT: A 349 ARG cc_start: 0.8901 (mtm-85) cc_final: 0.8614 (mtm-85) REVERT: A 363 MET cc_start: 0.8857 (mtt) cc_final: 0.8579 (mtt) REVERT: B 42 LYS cc_start: 0.8081 (mtmp) cc_final: 0.7842 (mtmt) REVERT: B 144 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8113 (mm-30) REVERT: B 380 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8342 (tp30) REVERT: B 406 LYS cc_start: 0.8485 (ttmm) cc_final: 0.7855 (mtmt) REVERT: C 48 LYS cc_start: 0.7667 (mmmt) cc_final: 0.7299 (mttp) REVERT: C 95 LYS cc_start: 0.7637 (mtpt) cc_final: 0.7198 (mttm) REVERT: C 99 GLU cc_start: 0.5992 (mm-30) cc_final: 0.5780 (mm-30) REVERT: C 156 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: C 215 GLU cc_start: 0.7136 (pm20) cc_final: 0.6689 (pt0) REVERT: D 17 ASP cc_start: 0.8473 (m-30) cc_final: 0.8208 (m-30) REVERT: D 49 MET cc_start: 0.8590 (mtp) cc_final: 0.8330 (mtm) REVERT: D 99 LYS cc_start: 0.8241 (mtmt) cc_final: 0.8020 (mtpt) REVERT: E 33 LYS cc_start: 0.8454 (mttt) cc_final: 0.8009 (mtmt) REVERT: E 92 GLN cc_start: 0.7880 (mt0) cc_final: 0.7472 (mt0) REVERT: F 80 ARG cc_start: 0.4676 (mtt-85) cc_final: 0.4146 (ptp90) REVERT: F 135 CYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5367 (p) REVERT: F 272 THR cc_start: 0.6114 (OUTLIER) cc_final: 0.5904 (p) REVERT: F 289 ARG cc_start: 0.5465 (ttt-90) cc_final: 0.5001 (tmt170) REVERT: F 291 HIS cc_start: 0.4086 (OUTLIER) cc_final: 0.3353 (m90) REVERT: F 309 TYR cc_start: 0.5900 (t80) cc_final: 0.5047 (t80) REVERT: F 317 MET cc_start: 0.6686 (mtt) cc_final: 0.6298 (mmt) outliers start: 38 outliers final: 21 residues processed: 221 average time/residue: 0.5816 time to fit residues: 140.4481 Evaluate side-chains 223 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 235 VAL 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 114 SER 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 156 GLU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 69 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 146 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 126 optimal weight: 0.0000 chunk 141 optimal weight: 3.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 202 GLN A 433 GLN C 68 ASN F 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.188797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.169622 restraints weight = 11936.718| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 0.69 r_work: 0.3654 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2039 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= 0.136 Angle : 0.558 13.074 20478 Z= 0.292 Chirality : 0.043 0.234 2320 Planarity : 0.005 0.060 2567 Dihedral : 6.577 59.750 2223 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.46 % Allowed : 14.95 % Favored : 82.59 % 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 are not related in a simple way. whole: 0.72 (0.19), residues: 1882 helix: 1.49 (0.17), residues: 866 sheet: 0.58 (0.40), residues: 166 loop : -0.59 (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 0.018 0.002 PHE D 50 TRP 0.019 0.002 TRP B 103 HIS 0.007 0.001 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (15081) covalent geometry : angle 0.55236 / 0.29 (20468) hydrogen bonds : bond 0.05021 / 3.29 ( 744) hydrogen bonds : angle 4.60196 / 3.19 ( 2103) metal coordination : bond 0.00804 / 0.39 ( 7) metal coordination : angle 3.64881 / 2.11 ( 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 236 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6444 (ttp) cc_final: 0.6095 (mtp) REVERT: A 349 ARG cc_start: 0.8802 (mtm-85) cc_final: 0.8569 (mtm-85) REVERT: A 363 MET cc_start: 0.8657 (mtt) cc_final: 0.8355 (mtt) REVERT: A 384 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7390 (tmm) REVERT: A 444 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6989 (ttpt) REVERT: B 42 LYS cc_start: 0.8008 (mtmp) cc_final: 0.7721 (mtmt) REVERT: B 380 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8307 (tp30) REVERT: B 406 LYS cc_start: 0.8417 (ttmm) cc_final: 0.7944 (mtmt) REVERT: D 17 ASP cc_start: 0.8513 (m-30) cc_final: 0.8257 (m-30) REVERT: D 49 MET cc_start: 0.8521 (mtp) cc_final: 0.8290 (mtm) REVERT: E 33 LYS cc_start: 0.8384 (mttt) cc_final: 0.8158 (mtmt) REVERT: E 92 GLN cc_start: 0.8389 (mt0) cc_final: 0.8157 (mt0) REVERT: F 229 ARG cc_start: 0.5514 (ttp-110) cc_final: 0.4924 (ttt180) REVERT: F 291 HIS cc_start: 0.5107 (OUTLIER) cc_final: 0.4413 (m90) outliers start: 38 outliers final: 22 residues processed: 221 average time/residue: 0.5740 time to fit residues: 138.7762 Evaluate side-chains 209 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 A residue 444 LYS 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 155 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 69 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 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: 3.9990 chunk 88 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 180 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 202 GLN A 433 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 = 0.3991 r_free = 0.3991 target = 0.186726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.166424 restraints weight = 11873.488| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 0.71 r_work: 0.3169 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15088 Z= 0.191 Angle : 0.635 13.049 20478 Z= 0.330 Chirality : 0.047 0.255 2320 Planarity : 0.005 0.056 2567 Dihedral : 6.951 59.907 2223 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.27 % Allowed : 15.66 % Favored : 82.07 % 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 are not related in a simple way. whole: 0.54 (0.19), residues: 1882 helix: 1.27 (0.17), residues: 866 sheet: 0.57 (0.39), residues: 166 loop : -0.61 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 229 TYR 0.016 0.002 TYR D 141 PHE 0.022 0.002 PHE F 11 TRP 0.019 0.002 TRP B 70 HIS 0.010 0.002 HIS F 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (15081) covalent geometry : angle 0.62903 / 0.33 (20468) hydrogen bonds : bond 0.05931 / 3.88 ( 744) hydrogen bonds : angle 4.75671 / 3.29 ( 2103) metal coordination : bond 0.01161 / 0.58 ( 7) metal coordination : angle 3.94823 / 2.27 ( 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 213 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6323 (ttp) cc_final: 0.5745 (mtp) REVERT: A 349 ARG cc_start: 0.8921 (mtm-85) cc_final: 0.8719 (mtm-85) REVERT: A 363 MET cc_start: 0.8846 (mtt) cc_final: 0.8600 (mtt) REVERT: A 384 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.7405 (tmm) REVERT: A 444 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6550 (ttpt) REVERT: B 42 LYS cc_start: 0.8122 (mtmp) cc_final: 0.7873 (mtmt) REVERT: B 380 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8410 (tp30) REVERT: B 406 LYS cc_start: 0.8480 (ttmm) cc_final: 0.7789 (mtmt) REVERT: D 17 ASP cc_start: 0.8487 (m-30) cc_final: 0.8224 (m-30) REVERT: D 49 MET cc_start: 0.8600 (mtp) cc_final: 0.8337 (mtm) REVERT: E 33 LYS cc_start: 0.8480 (mttt) cc_final: 0.8028 (mtmt) REVERT: E 92 GLN cc_start: 0.7947 (mt0) cc_final: 0.7531 (mt0) outliers start: 35 outliers final: 25 residues processed: 199 average time/residue: 0.5660 time to fit residues: 123.8444 Evaluate side-chains 207 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 A residue 444 LYS 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 155 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 69 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 136 THR Chi-restraints excluded: chain F residue 245 MET 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 94 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 170 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 202 GLN A 433 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 = 0.4022 r_free = 0.4022 target = 0.190029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.125531 restraints weight = 11874.595| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.92 r_work: 0.3022 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15088 Z= 0.115 Angle : 0.528 13.010 20478 Z= 0.277 Chirality : 0.042 0.234 2320 Planarity : 0.005 0.054 2567 Dihedral : 6.605 59.788 2223 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.55 % Allowed : 16.31 % Favored : 82.14 % 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 are not related in a simple way. whole: 0.88 (0.19), residues: 1882 helix: 1.67 (0.18), residues: 863 sheet: 0.56 (0.39), residues: 168 loop : -0.52 (0.20), residues: 851 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 0.017 0.001 PHE D 50 TRP 0.019 0.001 TRP B 100 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15081) covalent geometry : angle 0.52294 / 0.28 (20468) hydrogen bonds : bond 0.04406 / 2.89 ( 744) hydrogen bonds : angle 4.50086 / 3.11 ( 2103) metal coordination : bond 0.00659 / 0.32 ( 7) metal coordination : angle 3.23101 / 1.86 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5222.24 seconds wall clock time: 89 minutes 24.47 seconds (5364.47 seconds total)