Starting phenix.real_space_refine on Fri Jul 3 15:12:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u5g_63872/07_2026/9u5g_63872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u5g_63872/07_2026/9u5g_63872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u5g_63872/07_2026/9u5g_63872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u5g_63872/07_2026/9u5g_63872.map" model { file = "/net/cci-nas-00/data/ceres_data/9u5g_63872/07_2026/9u5g_63872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u5g_63872/07_2026/9u5g_63872.cif" } resolution = 2.66 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= 0.001 sd= 0.051 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 3 5.49 5 S 93 5.16 5 C 9543 2.51 5 N 2414 2.21 5 O 2707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 14765 Number of models: 1 Model: "" Number of chains: 13 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: {'CIS': 1, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 421} 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: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1950 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} 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: {'PTRANS': 24, 'TRANS': 383} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9136 SG CYS D 112 42.405 74.349 64.774 1.00100.28 S ATOM 10102 SG CYS E 26 44.682 71.658 66.109 1.00101.65 S ATOM 8497 SG CYS D 29 43.283 68.365 62.248 1.00101.31 S ATOM 10824 SG CYS E 120 41.821 71.159 60.346 1.00 95.55 S Time building chain proxies: 3.44, per 1000 atoms: 0.23 Number of scatterers: 14765 At special positions: 0 Unit cell: (89.76, 124.96, 154, 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 93 16.00 P 3 15.00 O 2707 8.00 N 2414 7.00 C 9543 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: 1.41 Conformation dependent library (CDL) restraints added in 595.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 301 " pdb="FE1 FES D 301 " - pdb=" SG CYS E 26 " pdb="FE2 FES D 301 " - pdb=" SG CYS E 120 " pdb="FE2 FES D 301 " - pdb=" SG CYS D 29 " pdb="FE1 FES D 301 " - pdb=" SG CYS D 112 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 70 " Number of angles added : 7 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 13 sheets defined 55.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' 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 113 removed outlier: 4.618A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.682A pdb=" N PHE A 131 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.549A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 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 335 through 339 Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.833A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) 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 446 removed outlier: 3.940A 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 151 removed outlier: 3.655A 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 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 244 removed outlier: 3.507A pdb=" N ALA B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.582A pdb=" N LEU B 249 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.517A pdb=" N GLU B 274 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 4.334A 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: 3.808A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.739A 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: 3.612A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.966A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.707A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 391 removed outlier: 3.833A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 410 Processing helix chain 'C' and resid 1 through 5 Processing helix chain 'C' and resid 7 through 33 removed outlier: 4.360A pdb=" N CYS C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 54 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 182 through 188 removed outlier: 3.669A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.573A pdb=" N PHE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'D' and resid 8 through 12 Processing helix chain 'D' and resid 12 through 17 removed outlier: 4.385A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 37 through 62 removed outlier: 3.654A pdb=" N ILE D 62 " --> pdb=" O PHE D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.828A 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 70 through 94 Processing helix chain 'D' and resid 94 through 102 removed outlier: 3.726A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.505A pdb=" N ILE D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 110' Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.121A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.514A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.621A 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 Processing helix chain 'D' and resid 183 through 201 removed outlier: 3.924A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.548A pdb=" N GLN D 205 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 31 removed outlier: 3.777A pdb=" N PHE E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) 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 removed outlier: 3.562A pdb=" N MET E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 111 through 117 Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.816A 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 170 through 174 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 removed outlier: 3.643A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY F 7 " --> pdb=" O THR F 3 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 63 removed outlier: 4.144A pdb=" N ALA F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.507A pdb=" N LEU F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.792A 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 106 Processing helix chain 'F' and resid 125 through 130 removed outlier: 3.517A pdb=" N PHE F 128 " --> pdb=" O GLU F 125 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL F 130 " --> pdb=" O ILE F 127 " (cutoff:3.500A) 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 188 through 196 removed outlier: 3.956A pdb=" N TRP F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (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 243 through 252 removed outlier: 4.013A pdb=" N SER F 247 " --> pdb=" O GLY F 243 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU F 252 " --> pdb=" O TYR F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.587A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 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 369 through 373 removed outlier: 3.769A pdb=" N CYS F 373 " --> pdb=" O PRO F 370 " (cutoff:3.500A) 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: 6.521A 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: 3.620A pdb=" N LEU A 274 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.611A pdb=" N ASN A 80 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL A 90 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU A 78 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 92 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 76 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 94 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.144A 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: 7.149A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 84 removed outlier: 4.218A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 169 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.501A pdb=" N LYS C 204 " --> pdb=" O VAL C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AB1, first strand: chain 'F' and resid 142 through 144 removed outlier: 5.637A pdb=" N ASN F 142 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLU F 149 " --> pdb=" O ASN F 142 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 139 " --> pdb=" O LYS F 151 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA F 153 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL F 137 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE F 260 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU F 171 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY F 262 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN F 169 " --> pdb=" O GLY F 262 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 142 through 144 removed outlier: 5.637A pdb=" N ASN F 142 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLU F 149 " --> pdb=" O ASN F 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB4, first strand: chain 'F' and resid 333 through 339 removed outlier: 6.905A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP F 404 " --> pdb=" O TYR F 375 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N MET F 377 " --> pdb=" O ASP F 404 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 2043 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: 2.58 Time building geometry restraints manager: 1.86 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: 6077 1.40 - 1.60: 8850 1.60 - 1.80: 140 1.80 - 2.00: 22 2.00 - 2.20: 8 Bond restraints: 15097 Sorted by residual: bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.401 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" O5' FMN B 501 " pdb=" P FMN B 501 " ideal model delta sigma weight residual 1.676 1.610 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C2 FMN B 501 " pdb=" N3 FMN B 501 " ideal model delta sigma weight residual 1.404 1.351 0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" N LEU D 7 " pdb=" CA LEU D 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N TYR B 27 " pdb=" CA TYR B 27 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 15092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 20267 2.49 - 4.99: 203 4.99 - 7.48: 12 7.48 - 9.98: 1 9.98 - 12.47: 1 Bond angle restraints: 20484 Sorted by residual: angle pdb=" C ALA A 314 " pdb=" N TYR A 315 " pdb=" CA TYR A 315 " ideal model delta sigma weight residual 121.70 134.17 -12.47 1.80e+00 3.09e-01 4.80e+01 angle pdb=" CA ALA A 314 " pdb=" C ALA A 314 " pdb=" N TYR A 315 " ideal model delta sigma weight residual 115.95 122.73 -6.78 1.39e+00 5.18e-01 2.38e+01 angle pdb=" C SER B 44 " pdb=" CA SER B 44 " pdb=" CB SER B 44 " ideal model delta sigma weight residual 117.23 110.73 6.50 1.36e+00 5.41e-01 2.28e+01 angle pdb=" N ALA A 314 " pdb=" CA ALA A 314 " pdb=" C ALA A 314 " ideal model delta sigma weight residual 109.56 115.96 -6.40 1.84e+00 2.95e-01 1.21e+01 angle pdb=" CB MET F 382 " pdb=" CG MET F 382 " pdb=" SD MET F 382 " ideal model delta sigma weight residual 112.70 122.67 -9.97 3.00e+00 1.11e-01 1.10e+01 ... (remaining 20479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8208 17.84 - 35.67: 574 35.67 - 53.51: 145 53.51 - 71.34: 31 71.34 - 89.18: 17 Dihedral angle restraints: 8975 sinusoidal: 3594 harmonic: 5381 Sorted by residual: dihedral pdb=" CA THR A 366 " pdb=" C THR A 366 " pdb=" N THR A 367 " pdb=" CA THR A 367 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LEU E 19 " pdb=" C LEU E 19 " pdb=" N SER E 20 " pdb=" CA SER E 20 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA THR C 227 " pdb=" C THR C 227 " pdb=" N SER C 228 " pdb=" CA SER C 228 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1883 0.056 - 0.112: 388 0.112 - 0.169: 50 0.169 - 0.225: 0 0.225 - 0.281: 1 Chirality restraints: 2322 Sorted by residual: chirality pdb=" CA TYR A 315 " pdb=" N TYR A 315 " pdb=" C TYR A 315 " pdb=" CB TYR A 315 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 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 5.06e-01 chirality pdb=" CA ILE A 239 " pdb=" N ILE A 239 " pdb=" C ILE A 239 " pdb=" CB ILE A 239 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2319 not shown) Planarity restraints: 2575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 226 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C LEU C 226 " 0.069 2.00e-02 2.50e+03 pdb=" O LEU C 226 " -0.026 2.00e-02 2.50e+03 pdb=" N THR C 227 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 22 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C CYS C 22 " 0.067 2.00e-02 2.50e+03 pdb=" O CYS C 22 " -0.025 2.00e-02 2.50e+03 pdb=" N SER C 23 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 126 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" CD GLU F 126 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU F 126 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU F 126 " -0.011 2.00e-02 2.50e+03 ... (remaining 2572 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 189 2.67 - 3.23: 14527 3.23 - 3.78: 22153 3.78 - 4.34: 31800 4.34 - 4.90: 52541 Nonbonded interactions: 121210 Sorted by model distance: nonbonded pdb=" N GLU E 2 " pdb=" OE1 GLU E 2 " model vdw 2.111 3.120 nonbonded pdb=" N GLU E 71 " pdb=" OE1 GLU E 71 " model vdw 2.124 3.120 nonbonded pdb=" O SER C 19 " pdb=" OG SER C 23 " model vdw 2.131 3.040 nonbonded pdb=" O3P FMN B 501 " pdb=" O4' FMN B 501 " model vdw 2.135 3.040 nonbonded pdb=" NE ARG F 210 " pdb=" O1P FAD F 502 " model vdw 2.208 3.120 ... (remaining 121205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.040 Set scattering table: 0.040 Process input model: 17.340 Find NCS groups from input model: 0.080 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 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 : 0.009 0.969 15102 Z= 0.271 Angle : 0.638 27.860 20491 Z= 0.335 Chirality : 0.045 0.281 2322 Planarity : 0.004 0.040 2575 Dihedral : 14.004 89.176 5543 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.90 % Allowed : 9.94 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.73 (0.19), residues: 1888 helix: 1.48 (0.18), residues: 867 sheet: -0.36 (0.37), residues: 176 loop : -0.31 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.017 0.001 TYR D 141 PHE 0.014 0.001 PHE E 22 TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (15097) covalent geometry : angle 0.60467 / 0.33 (20484) hydrogen bonds : bond 0.13478 / 8.97 ( 729) hydrogen bonds : angle 5.68729 / 4.02 ( 2043) metal coordination : bond 0.43347 / 34.13 ( 5) metal coordination : angle 10.98090 / 6.32 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 266 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7213 (mppt) cc_final: 0.7012 (mppt) REVERT: A 50 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6771 (mt-10) REVERT: A 52 LYS cc_start: 0.6881 (mttm) cc_final: 0.6627 (mtpt) REVERT: A 67 LYS cc_start: 0.7438 (mttt) cc_final: 0.7226 (mttp) REVERT: A 93 GLU cc_start: 0.7187 (tt0) cc_final: 0.6874 (tt0) REVERT: A 101 THR cc_start: 0.7290 (m) cc_final: 0.7046 (p) REVERT: A 104 LYS cc_start: 0.7307 (ptmm) cc_final: 0.7107 (ptmt) REVERT: A 106 GLU cc_start: 0.6508 (mt-10) cc_final: 0.6055 (mm-30) REVERT: A 109 GLN cc_start: 0.6494 (mt0) cc_final: 0.6268 (mt0) REVERT: A 172 GLU cc_start: 0.5605 (tt0) cc_final: 0.4940 (mt-10) REVERT: A 271 LYS cc_start: 0.6839 (mttm) cc_final: 0.6413 (mtpp) REVERT: A 284 GLU cc_start: 0.6932 (tt0) cc_final: 0.5898 (mm-30) REVERT: A 414 ASP cc_start: 0.6289 (t70) cc_final: 0.5880 (t0) REVERT: B 106 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6286 (mm-30) REVERT: B 252 ASN cc_start: 0.7316 (m-40) cc_final: 0.7038 (m-40) REVERT: B 265 ILE cc_start: 0.6691 (mt) cc_final: 0.6486 (mm) REVERT: C 58 LYS cc_start: 0.6210 (mtpp) cc_final: 0.5754 (mttt) REVERT: C 95 LYS cc_start: 0.5694 (mtpp) cc_final: 0.5352 (mtpp) REVERT: C 204 LYS cc_start: 0.6157 (mmmm) cc_final: 0.5735 (mmtt) REVERT: D 69 SER cc_start: 0.6131 (m) cc_final: 0.5912 (p) REVERT: D 159 LYS cc_start: 0.6053 (mtmm) cc_final: 0.5643 (mttt) REVERT: E 27 THR cc_start: 0.6820 (t) cc_final: 0.6364 (p) REVERT: E 43 ILE cc_start: 0.6095 (mm) cc_final: 0.5867 (mt) REVERT: F 1 MET cc_start: 0.5302 (tpp) cc_final: 0.4857 (tpp) REVERT: F 82 LYS cc_start: 0.6424 (tttm) cc_final: 0.5884 (tmtt) REVERT: F 119 MET cc_start: 0.4970 (ptt) cc_final: 0.4621 (ptt) REVERT: F 214 MET cc_start: 0.5582 (mtm) cc_final: 0.5300 (mpp) REVERT: F 229 ARG cc_start: 0.5358 (tpt90) cc_final: 0.5124 (ttp-170) REVERT: F 252 LEU cc_start: 0.5467 (mm) cc_final: 0.4930 (mt) REVERT: F 253 LYS cc_start: 0.3671 (mmtp) cc_final: 0.3045 (ptpp) REVERT: F 302 LYS cc_start: 0.6352 (mmtp) cc_final: 0.5988 (mtmt) REVERT: F 305 MET cc_start: 0.6707 (ptp) cc_final: 0.6151 (ptt) REVERT: F 309 TYR cc_start: 0.5317 (t80) cc_final: 0.5086 (t80) REVERT: F 317 MET cc_start: 0.6686 (ptp) cc_final: 0.6037 (mtp) REVERT: F 320 VAL cc_start: 0.5691 (m) cc_final: 0.5416 (t) REVERT: F 337 CYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7029 (m) REVERT: F 361 GLU cc_start: 0.5667 (mm-30) cc_final: 0.5240 (mt-10) REVERT: F 377 MET cc_start: 0.6391 (ttp) cc_final: 0.6015 (ttm) REVERT: F 392 LYS cc_start: 0.6867 (mtpp) cc_final: 0.6662 (mtpp) outliers start: 14 outliers final: 9 residues processed: 277 average time/residue: 0.5748 time to fit residues: 175.3421 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.1980 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 HIS E 131 GLN F 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.179679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.126551 restraints weight = 12990.890| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.62 r_work: 0.3081 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15102 Z= 0.135 Angle : 0.593 13.272 20491 Z= 0.314 Chirality : 0.044 0.270 2322 Planarity : 0.005 0.040 2575 Dihedral : 7.189 95.113 2227 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.13 % Allowed : 12.45 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.77 (0.19), residues: 1888 helix: 1.64 (0.18), residues: 861 sheet: -0.25 (0.37), residues: 166 loop : -0.45 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 104 TYR 0.017 0.001 TYR D 141 PHE 0.020 0.002 PHE F 267 TRP 0.021 0.002 TRP B 103 HIS 0.005 0.001 HIS E 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (15097) covalent geometry : angle 0.58404 / 0.31 (20484) hydrogen bonds : bond 0.05043 / 3.40 ( 729) hydrogen bonds : angle 4.85141 / 3.41 ( 2043) metal coordination : bond 0.00694 / 0.47 ( 5) metal coordination : angle 5.53467 / 2.93 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7618 (mt-10) REVERT: A 104 LYS cc_start: 0.8703 (ptmm) cc_final: 0.8487 (ptmt) REVERT: A 106 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7701 (mm-30) REVERT: A 284 GLU cc_start: 0.8282 (tt0) cc_final: 0.7915 (mm-30) REVERT: A 442 ILE cc_start: 0.8068 (mm) cc_final: 0.7828 (mm) REVERT: A 445 GLU cc_start: 0.6528 (pt0) cc_final: 0.6169 (pp20) REVERT: B 106 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8193 (mm-30) REVERT: B 252 ASN cc_start: 0.8630 (m-40) cc_final: 0.8368 (m-40) REVERT: C 58 LYS cc_start: 0.7048 (mtpp) cc_final: 0.6612 (mttt) REVERT: C 95 LYS cc_start: 0.7183 (mtpp) cc_final: 0.6775 (mtpp) REVERT: C 115 ILE cc_start: 0.4947 (mt) cc_final: 0.4564 (pt) REVERT: C 200 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7576 (mptm) REVERT: C 204 LYS cc_start: 0.7672 (mmmm) cc_final: 0.7330 (mmtt) REVERT: D 39 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: D 159 LYS cc_start: 0.8729 (mtmm) cc_final: 0.8385 (mttt) REVERT: E 27 THR cc_start: 0.8745 (t) cc_final: 0.8363 (p) REVERT: E 43 ILE cc_start: 0.8905 (mm) cc_final: 0.8665 (mt) REVERT: E 65 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7239 (ttmm) REVERT: F 1 MET cc_start: 0.6809 (tpp) cc_final: 0.6369 (tpp) REVERT: F 82 LYS cc_start: 0.7096 (tttm) cc_final: 0.6452 (tmtt) REVERT: F 214 MET cc_start: 0.6488 (mtm) cc_final: 0.5932 (mpp) REVERT: F 252 LEU cc_start: 0.6235 (mm) cc_final: 0.5733 (mt) REVERT: F 253 LYS cc_start: 0.3799 (mmtp) cc_final: 0.3457 (ptpt) REVERT: F 302 LYS cc_start: 0.6518 (mmtp) cc_final: 0.6290 (mtmt) REVERT: F 305 MET cc_start: 0.7738 (ptp) cc_final: 0.7062 (mtm) REVERT: F 309 TYR cc_start: 0.6628 (t80) cc_final: 0.6355 (t80) REVERT: F 317 MET cc_start: 0.7023 (ptp) cc_final: 0.6392 (mtp) REVERT: F 361 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6185 (mt-10) REVERT: F 377 MET cc_start: 0.7519 (ttp) cc_final: 0.7081 (ttm) REVERT: F 398 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6979 (tp30) outliers start: 33 outliers final: 10 residues processed: 232 average time/residue: 0.5952 time to fit residues: 151.8615 Evaluate side-chains 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 32 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 ASN B 156 ASN E 131 GLN F 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.174104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138732 restraints weight = 13059.521| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.10 r_work: 0.3041 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15102 Z= 0.257 Angle : 0.733 16.287 20491 Z= 0.388 Chirality : 0.052 0.338 2322 Planarity : 0.006 0.054 2575 Dihedral : 7.499 71.768 2220 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.87 % Allowed : 12.26 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.11 (0.18), residues: 1888 helix: 0.95 (0.17), residues: 863 sheet: -0.28 (0.38), residues: 157 loop : -0.70 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 407 TYR 0.024 0.003 TYR A 315 PHE 0.033 0.003 PHE F 267 TRP 0.021 0.003 TRP B 70 HIS 0.007 0.002 HIS E 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.26 (15097) covalent geometry : angle 0.72886 / 0.39 (20484) hydrogen bonds : bond 0.07203 / 4.81 ( 729) hydrogen bonds : angle 5.08037 / 3.58 ( 2043) metal coordination : bond 0.01644 / 0.90 ( 5) metal coordination : angle 4.19499 / 1.90 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 182 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8858 (ptmm) cc_final: 0.8509 (ptpt) REVERT: A 233 ASP cc_start: 0.8348 (m-30) cc_final: 0.8051 (m-30) REVERT: A 284 GLU cc_start: 0.8372 (tt0) cc_final: 0.8065 (mm-30) REVERT: A 331 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.5927 (p0) REVERT: A 384 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.7853 (tmm) REVERT: A 441 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7772 (ttmt) REVERT: A 445 GLU cc_start: 0.6742 (pt0) cc_final: 0.6377 (pp20) REVERT: B 106 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8344 (mm-30) REVERT: C 58 LYS cc_start: 0.6964 (mtpp) cc_final: 0.6668 (mtmt) REVERT: C 95 LYS cc_start: 0.7481 (mtpp) cc_final: 0.7028 (mttp) REVERT: C 149 MET cc_start: 0.8926 (mtm) cc_final: 0.8610 (mtm) REVERT: C 200 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7802 (mptm) REVERT: C 204 LYS cc_start: 0.7817 (mmmm) cc_final: 0.7407 (mmtt) REVERT: D 39 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: D 159 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8572 (mttt) REVERT: E 27 THR cc_start: 0.8790 (t) cc_final: 0.8381 (p) REVERT: E 65 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7207 (ttmt) REVERT: F 82 LYS cc_start: 0.7417 (tttm) cc_final: 0.6758 (tmtt) REVERT: F 91 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6718 (tt) REVERT: F 148 LYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6442 (ptpt) REVERT: F 214 MET cc_start: 0.6840 (mtm) cc_final: 0.6042 (mpp) REVERT: F 229 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.5569 (ttp-170) REVERT: F 252 LEU cc_start: 0.6323 (mm) cc_final: 0.5543 (tt) REVERT: F 253 LYS cc_start: 0.3836 (mmtp) cc_final: 0.3606 (ptpt) REVERT: F 305 MET cc_start: 0.7804 (ptp) cc_final: 0.7230 (mtm) REVERT: F 309 TYR cc_start: 0.6852 (t80) cc_final: 0.6513 (t80) REVERT: F 317 MET cc_start: 0.7058 (ptp) cc_final: 0.6458 (mtp) REVERT: F 361 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6481 (mt-10) REVERT: F 377 MET cc_start: 0.7850 (ttp) cc_final: 0.7640 (ttm) REVERT: F 390 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7356 (tmm) outliers start: 60 outliers final: 30 residues processed: 221 average time/residue: 0.5860 time to fit residues: 141.9534 Evaluate side-chains 211 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 229 ARG Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 390 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 39 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.176743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137771 restraints weight = 12978.728| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.16 r_work: 0.3079 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15102 Z= 0.157 Angle : 0.605 13.992 20491 Z= 0.322 Chirality : 0.045 0.301 2322 Planarity : 0.005 0.046 2575 Dihedral : 7.257 84.990 2220 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.03 % Allowed : 13.42 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.29 (0.19), residues: 1888 helix: 1.16 (0.18), residues: 866 sheet: -0.23 (0.39), residues: 157 loop : -0.68 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 210 TYR 0.019 0.002 TYR D 141 PHE 0.040 0.002 PHE F 267 TRP 0.022 0.002 TRP B 103 HIS 0.004 0.001 HIS E 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (15097) covalent geometry : angle 0.60104 / 0.32 (20484) hydrogen bonds : bond 0.05577 / 3.73 ( 729) hydrogen bonds : angle 4.83524 / 3.40 ( 2043) metal coordination : bond 0.00923 / 0.50 ( 5) metal coordination : angle 3.86214 / 1.85 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8850 (ptmm) cc_final: 0.8473 (ptpt) REVERT: A 284 GLU cc_start: 0.8345 (tt0) cc_final: 0.8027 (mm-30) REVERT: A 384 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.7859 (tmm) REVERT: A 441 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7698 (ttmt) REVERT: A 445 GLU cc_start: 0.6574 (pt0) cc_final: 0.6255 (pp20) REVERT: B 106 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8343 (mm-30) REVERT: B 406 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8339 (mttt) REVERT: C 58 LYS cc_start: 0.6978 (mtpp) cc_final: 0.6701 (mttt) REVERT: C 95 LYS cc_start: 0.7409 (mtpp) cc_final: 0.7000 (mtpp) REVERT: C 106 LEU cc_start: 0.7222 (pt) cc_final: 0.5933 (tm) REVERT: C 149 MET cc_start: 0.8887 (mtm) cc_final: 0.8576 (mtm) REVERT: C 200 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7685 (mptm) REVERT: C 204 LYS cc_start: 0.7761 (mmmm) cc_final: 0.7288 (mmtt) REVERT: D 39 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: D 159 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8563 (mttt) REVERT: E 27 THR cc_start: 0.8763 (t) cc_final: 0.8425 (p) REVERT: E 65 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7326 (ttmm) REVERT: E 100 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7979 (tpt90) REVERT: E 190 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7755 (t80) REVERT: F 82 LYS cc_start: 0.7409 (tttm) cc_final: 0.6747 (tmtt) REVERT: F 90 ILE cc_start: 0.7140 (mp) cc_final: 0.6688 (tt) REVERT: F 91 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6573 (tt) REVERT: F 214 MET cc_start: 0.6727 (mtm) cc_final: 0.5925 (mpp) REVERT: F 225 MET cc_start: 0.4741 (mtp) cc_final: 0.4366 (mmm) REVERT: F 252 LEU cc_start: 0.6230 (mm) cc_final: 0.5429 (tt) REVERT: F 253 LYS cc_start: 0.3879 (mmtp) cc_final: 0.3595 (ptpt) REVERT: F 305 MET cc_start: 0.7756 (ptp) cc_final: 0.7255 (mtm) REVERT: F 309 TYR cc_start: 0.6870 (t80) cc_final: 0.6538 (t80) REVERT: F 317 MET cc_start: 0.7150 (ptp) cc_final: 0.6425 (mtp) REVERT: F 361 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6445 (mt-10) outliers start: 47 outliers final: 25 residues processed: 213 average time/residue: 0.6045 time to fit residues: 140.7909 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 313 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 146 optimal weight: 0.0980 chunk 138 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 180 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN F 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.174897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121386 restraints weight = 13027.450| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.47 r_work: 0.2963 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15102 Z= 0.221 Angle : 0.679 15.573 20491 Z= 0.360 Chirality : 0.049 0.332 2322 Planarity : 0.006 0.050 2575 Dihedral : 7.487 97.902 2220 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.94 % Allowed : 13.55 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.10 (0.19), residues: 1888 helix: 0.94 (0.17), residues: 865 sheet: -0.25 (0.39), residues: 157 loop : -0.73 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 46 TYR 0.023 0.002 TYR A 315 PHE 0.030 0.002 PHE F 267 TRP 0.021 0.003 TRP B 103 HIS 0.006 0.002 HIS E 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (15097) covalent geometry : angle 0.67571 / 0.36 (20484) hydrogen bonds : bond 0.06626 / 4.43 ( 729) hydrogen bonds : angle 4.95894 / 3.48 ( 2043) metal coordination : bond 0.01440 / 0.73 ( 5) metal coordination : angle 3.85742 / 1.71 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 0.594 Fit side-chains REVERT: A 104 LYS cc_start: 0.8877 (ptmm) cc_final: 0.8633 (ptmt) REVERT: A 284 GLU cc_start: 0.8433 (tt0) cc_final: 0.8042 (mm-30) REVERT: A 331 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.5856 (p0) REVERT: A 384 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.7829 (tmm) REVERT: A 441 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7774 (ttmt) REVERT: A 445 GLU cc_start: 0.6647 (pt0) cc_final: 0.6309 (pp20) REVERT: B 42 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8133 (mtpt) REVERT: B 106 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8384 (mm-30) REVERT: C 36 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7727 (mtpt) REVERT: C 58 LYS cc_start: 0.7011 (mtpp) cc_final: 0.6713 (mttt) REVERT: C 95 LYS cc_start: 0.7413 (mtpp) cc_final: 0.6976 (mtpp) REVERT: C 106 LEU cc_start: 0.7199 (pt) cc_final: 0.5941 (tm) REVERT: C 149 MET cc_start: 0.8891 (mtm) cc_final: 0.8545 (mtm) REVERT: C 200 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7892 (mptm) REVERT: C 204 LYS cc_start: 0.7984 (mmmm) cc_final: 0.7511 (mmpt) REVERT: D 39 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: D 99 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7415 (mmpt) REVERT: D 159 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8605 (mttt) REVERT: E 100 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8174 (tpt90) REVERT: F 82 LYS cc_start: 0.7490 (tttm) cc_final: 0.6825 (tmtt) REVERT: F 91 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6489 (tt) REVERT: F 214 MET cc_start: 0.6791 (mtm) cc_final: 0.6054 (mpp) REVERT: F 225 MET cc_start: 0.4725 (mtp) cc_final: 0.4424 (mmm) REVERT: F 252 LEU cc_start: 0.6056 (mm) cc_final: 0.5249 (tt) REVERT: F 253 LYS cc_start: 0.3903 (mmtp) cc_final: 0.3633 (ptpt) REVERT: F 305 MET cc_start: 0.7728 (ptp) cc_final: 0.7190 (mtm) REVERT: F 309 TYR cc_start: 0.6784 (t80) cc_final: 0.6356 (t80) REVERT: F 317 MET cc_start: 0.7126 (ptp) cc_final: 0.6282 (mtp) REVERT: F 361 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6333 (mt-10) outliers start: 61 outliers final: 29 residues processed: 217 average time/residue: 0.6349 time to fit residues: 150.9158 Evaluate side-chains 207 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 304 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 83 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN C 188 GLN E 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.177126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.123859 restraints weight = 12921.171| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.52 r_work: 0.3038 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15102 Z= 0.143 Angle : 0.580 13.544 20491 Z= 0.310 Chirality : 0.044 0.292 2322 Planarity : 0.005 0.048 2575 Dihedral : 7.224 102.436 2220 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.84 % Allowed : 14.84 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.38 (0.19), residues: 1888 helix: 1.18 (0.18), residues: 873 sheet: -0.18 (0.39), residues: 164 loop : -0.59 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 46 TYR 0.020 0.001 TYR D 141 PHE 0.046 0.002 PHE F 267 TRP 0.022 0.002 TRP B 103 HIS 0.004 0.001 HIS E 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15097) covalent geometry : angle 0.57626 / 0.31 (20484) hydrogen bonds : bond 0.05261 / 3.52 ( 729) hydrogen bonds : angle 4.75059 / 3.33 ( 2043) metal coordination : bond 0.00760 / 0.40 ( 5) metal coordination : angle 3.36714 / 1.55 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8886 (ptmm) cc_final: 0.8644 (ptmt) REVERT: A 233 ASP cc_start: 0.8323 (m-30) cc_final: 0.8048 (m-30) REVERT: A 284 GLU cc_start: 0.8412 (tt0) cc_final: 0.8007 (mm-30) REVERT: A 331 ASP cc_start: 0.6840 (OUTLIER) cc_final: 0.5821 (p0) REVERT: A 384 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.7891 (tmm) REVERT: B 42 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8107 (mtpt) REVERT: B 106 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8366 (mm-30) REVERT: C 58 LYS cc_start: 0.7011 (mtpp) cc_final: 0.6691 (mttt) REVERT: C 95 LYS cc_start: 0.7318 (mtpp) cc_final: 0.6905 (mtpp) REVERT: C 106 LEU cc_start: 0.7019 (pt) cc_final: 0.5788 (tm) REVERT: C 149 MET cc_start: 0.8871 (mtm) cc_final: 0.8541 (mtm) REVERT: C 204 LYS cc_start: 0.7904 (mmmm) cc_final: 0.7447 (mmtt) REVERT: D 39 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: D 99 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7361 (mmpt) REVERT: D 159 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8569 (mttt) REVERT: E 100 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7848 (tpt90) REVERT: E 190 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7836 (t80) REVERT: F 82 LYS cc_start: 0.7535 (tttm) cc_final: 0.6864 (tmtt) REVERT: F 91 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6521 (tt) REVERT: F 214 MET cc_start: 0.6798 (mtm) cc_final: 0.5878 (mpp) REVERT: F 225 MET cc_start: 0.4633 (mtp) cc_final: 0.4433 (mmm) REVERT: F 252 LEU cc_start: 0.5942 (mm) cc_final: 0.5136 (tt) REVERT: F 253 LYS cc_start: 0.4047 (mmtp) cc_final: 0.3749 (ptpt) REVERT: F 305 MET cc_start: 0.7750 (ptp) cc_final: 0.7251 (mtm) REVERT: F 309 TYR cc_start: 0.6989 (t80) cc_final: 0.6460 (t80) REVERT: F 317 MET cc_start: 0.7067 (ptp) cc_final: 0.6272 (mtp) REVERT: F 361 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6306 (mt-10) outliers start: 44 outliers final: 26 residues processed: 206 average time/residue: 0.6265 time to fit residues: 142.0728 Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 331 ASP Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 340 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 115 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 132 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN C 188 GLN E 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.178049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141530 restraints weight = 12913.012| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.16 r_work: 0.3104 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15102 Z= 0.136 Angle : 0.566 13.206 20491 Z= 0.302 Chirality : 0.044 0.281 2322 Planarity : 0.005 0.050 2575 Dihedral : 6.962 105.061 2220 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.10 % Allowed : 14.58 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.47 (0.19), residues: 1888 helix: 1.31 (0.18), residues: 870 sheet: -0.07 (0.40), residues: 152 loop : -0.62 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 46 TYR 0.019 0.001 TYR D 141 PHE 0.037 0.002 PHE F 267 TRP 0.023 0.002 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (15097) covalent geometry : angle 0.56275 / 0.30 (20484) hydrogen bonds : bond 0.05039 / 3.37 ( 729) hydrogen bonds : angle 4.64648 / 3.26 ( 2043) metal coordination : bond 0.00632 / 0.33 ( 5) metal coordination : angle 3.07416 / 1.33 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.8901 (ptmm) cc_final: 0.8671 (ptmt) REVERT: A 147 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7814 (mm-30) REVERT: A 284 GLU cc_start: 0.8345 (tt0) cc_final: 0.8047 (mm-30) REVERT: A 331 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.5896 (p0) REVERT: A 441 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7788 (ttmt) REVERT: B 42 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8106 (mtpt) REVERT: B 106 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8345 (mm-30) REVERT: C 58 LYS cc_start: 0.6995 (mtpp) cc_final: 0.6695 (mttt) REVERT: C 95 LYS cc_start: 0.7305 (mtpp) cc_final: 0.6901 (mtpp) REVERT: C 106 LEU cc_start: 0.7010 (pt) cc_final: 0.5742 (tm) REVERT: C 149 MET cc_start: 0.8890 (mtm) cc_final: 0.8549 (mtm) REVERT: C 204 LYS cc_start: 0.7935 (mmmm) cc_final: 0.7483 (mmtt) REVERT: D 39 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: D 99 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7477 (mmpt) REVERT: D 159 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8579 (mttt) REVERT: E 27 THR cc_start: 0.8724 (t) cc_final: 0.8466 (p) REVERT: E 190 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7811 (t80) REVERT: F 82 LYS cc_start: 0.7526 (tttm) cc_final: 0.6880 (tmtt) REVERT: F 91 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6691 (tt) REVERT: F 214 MET cc_start: 0.6913 (mtm) cc_final: 0.6119 (mpp) REVERT: F 225 MET cc_start: 0.4732 (mtp) cc_final: 0.4445 (mmm) REVERT: F 252 LEU cc_start: 0.5974 (mm) cc_final: 0.5140 (tt) REVERT: F 253 LYS cc_start: 0.4239 (mmtp) cc_final: 0.3924 (ptpt) REVERT: F 305 MET cc_start: 0.7755 (ptp) cc_final: 0.7345 (mtm) REVERT: F 309 TYR cc_start: 0.7009 (t80) cc_final: 0.6540 (t80) REVERT: F 317 MET cc_start: 0.7057 (ptp) cc_final: 0.6255 (mtp) REVERT: F 361 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6413 (mt-10) outliers start: 48 outliers final: 30 residues processed: 210 average time/residue: 0.5829 time to fit residues: 134.3541 Evaluate side-chains 207 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 340 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 166 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 177 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 GLN E 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.174055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121314 restraints weight = 12963.722| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.38 r_work: 0.2946 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 15102 Z= 0.278 Angle : 0.737 16.260 20491 Z= 0.390 Chirality : 0.052 0.352 2322 Planarity : 0.006 0.054 2575 Dihedral : 7.443 109.625 2220 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.61 % Allowed : 14.26 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.01 (0.19), residues: 1888 helix: 0.84 (0.17), residues: 865 sheet: -0.29 (0.41), residues: 153 loop : -0.74 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 46 TYR 0.027 0.003 TYR A 315 PHE 0.055 0.003 PHE F 267 TRP 0.021 0.003 TRP B 70 HIS 0.007 0.002 HIS E 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.28 (15097) covalent geometry : angle 0.73342 / 0.39 (20484) hydrogen bonds : bond 0.07274 / 4.86 ( 729) hydrogen bonds : angle 4.98908 / 3.51 ( 2043) metal coordination : bond 0.01982 / 1.00 ( 5) metal coordination : angle 3.74387 / 1.57 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 0.551 Fit side-chains REVERT: A 104 LYS cc_start: 0.8886 (ptmm) cc_final: 0.8649 (ptmt) REVERT: A 284 GLU cc_start: 0.8418 (tt0) cc_final: 0.7987 (mm-30) REVERT: A 384 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.7958 (tmm) REVERT: A 441 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7736 (ttmt) REVERT: A 445 GLU cc_start: 0.6628 (pt0) cc_final: 0.6260 (pp20) REVERT: B 42 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8114 (mtpt) REVERT: B 106 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8379 (mm-30) REVERT: B 406 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8089 (mttt) REVERT: C 58 LYS cc_start: 0.7032 (mtpp) cc_final: 0.6812 (mttt) REVERT: C 95 LYS cc_start: 0.7330 (mtpp) cc_final: 0.6897 (mtpp) REVERT: C 106 LEU cc_start: 0.7117 (pt) cc_final: 0.5795 (tm) REVERT: C 149 MET cc_start: 0.8900 (mtm) cc_final: 0.8579 (mtm) REVERT: D 39 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: D 99 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7446 (mmpt) REVERT: D 159 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8609 (mttt) REVERT: E 27 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8421 (p) REVERT: E 100 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8088 (tpt90) REVERT: F 82 LYS cc_start: 0.7498 (tttm) cc_final: 0.6814 (tmtt) REVERT: F 91 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6484 (tt) REVERT: F 214 MET cc_start: 0.6963 (mtm) cc_final: 0.6278 (mpp) REVERT: F 225 MET cc_start: 0.4699 (mtp) cc_final: 0.4262 (mmm) REVERT: F 252 LEU cc_start: 0.5985 (mm) cc_final: 0.5188 (tt) REVERT: F 253 LYS cc_start: 0.4277 (mmtp) cc_final: 0.3878 (ptpp) REVERT: F 305 MET cc_start: 0.7681 (ptp) cc_final: 0.7159 (mtm) REVERT: F 309 TYR cc_start: 0.6925 (t80) cc_final: 0.6314 (t80) REVERT: F 317 MET cc_start: 0.7040 (ptp) cc_final: 0.6214 (mtp) REVERT: F 361 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6319 (mt-10) outliers start: 56 outliers final: 32 residues processed: 202 average time/residue: 0.5666 time to fit residues: 125.5305 Evaluate side-chains 208 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 340 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 62 GLN C 188 GLN E 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.177885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.139306 restraints weight = 13014.099| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.32 r_work: 0.3091 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15102 Z= 0.134 Angle : 0.571 13.408 20491 Z= 0.305 Chirality : 0.044 0.290 2322 Planarity : 0.005 0.050 2575 Dihedral : 6.924 107.503 2217 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.06 % Allowed : 16.06 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.37 (0.19), residues: 1888 helix: 1.20 (0.18), residues: 872 sheet: -0.14 (0.40), residues: 152 loop : -0.62 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 46 TYR 0.020 0.001 TYR D 141 PHE 0.050 0.002 PHE F 267 TRP 0.022 0.002 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (15097) covalent geometry : angle 0.56846 / 0.31 (20484) hydrogen bonds : bond 0.05095 / 3.41 ( 729) hydrogen bonds : angle 4.68613 / 3.29 ( 2043) metal coordination : bond 0.00640 / 0.33 ( 5) metal coordination : angle 3.10305 / 1.32 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.423 Fit side-chains REVERT: A 46 ARG cc_start: 0.8280 (ptp-110) cc_final: 0.7375 (ptp90) REVERT: A 104 LYS cc_start: 0.8911 (ptmm) cc_final: 0.8678 (ptmt) REVERT: A 284 GLU cc_start: 0.8444 (tt0) cc_final: 0.8060 (mm-30) REVERT: A 441 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7735 (ttmt) REVERT: A 445 GLU cc_start: 0.6627 (pt0) cc_final: 0.6283 (pp20) REVERT: B 42 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8134 (mtpt) REVERT: B 106 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8355 (mm-30) REVERT: B 406 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8107 (mttt) REVERT: C 58 LYS cc_start: 0.7015 (mtpp) cc_final: 0.6723 (mttt) REVERT: C 95 LYS cc_start: 0.7305 (mtpp) cc_final: 0.6886 (mtpp) REVERT: C 106 LEU cc_start: 0.6943 (pt) cc_final: 0.5683 (tm) REVERT: C 149 MET cc_start: 0.8936 (mtm) cc_final: 0.8630 (mtm) REVERT: D 39 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: D 99 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7495 (mmpt) REVERT: D 159 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8614 (mttt) REVERT: E 27 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8492 (p) REVERT: E 100 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7851 (tpt90) REVERT: F 82 LYS cc_start: 0.7546 (tttm) cc_final: 0.6905 (tmtt) REVERT: F 91 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6698 (tt) REVERT: F 214 MET cc_start: 0.6936 (mtm) cc_final: 0.6055 (mpp) REVERT: F 225 MET cc_start: 0.4755 (mtp) cc_final: 0.4451 (mmm) REVERT: F 245 MET cc_start: 0.3960 (tpp) cc_final: 0.3538 (tpp) REVERT: F 252 LEU cc_start: 0.5968 (mm) cc_final: 0.5153 (tt) REVERT: F 253 LYS cc_start: 0.4355 (mmtp) cc_final: 0.3990 (ptpp) REVERT: F 305 MET cc_start: 0.7761 (ptp) cc_final: 0.7352 (mtm) REVERT: F 309 TYR cc_start: 0.6988 (t80) cc_final: 0.6462 (t80) REVERT: F 317 MET cc_start: 0.7042 (ptp) cc_final: 0.6271 (mtp) REVERT: F 361 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6437 (mt-10) outliers start: 32 outliers final: 22 residues processed: 188 average time/residue: 0.6179 time to fit residues: 126.8568 Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 340 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 GLN E 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.177039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.140358 restraints weight = 12943.837| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.17 r_work: 0.3085 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15102 Z= 0.156 Angle : 0.594 13.521 20491 Z= 0.316 Chirality : 0.045 0.311 2322 Planarity : 0.005 0.055 2575 Dihedral : 6.875 108.133 2217 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.71 % Allowed : 15.42 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.34 (0.19), residues: 1888 helix: 1.17 (0.18), residues: 878 sheet: -0.29 (0.40), residues: 157 loop : -0.62 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 46 TYR 0.020 0.002 TYR D 141 PHE 0.049 0.002 PHE F 267 TRP 0.022 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (15097) covalent geometry : angle 0.59120 / 0.32 (20484) hydrogen bonds : bond 0.05480 / 3.66 ( 729) hydrogen bonds : angle 4.69530 / 3.30 ( 2043) metal coordination : bond 0.00799 / 0.41 ( 5) metal coordination : angle 3.17106 / 1.28 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.607 Fit side-chains REVERT: A 104 LYS cc_start: 0.8891 (ptmm) cc_final: 0.8656 (ptmt) REVERT: A 284 GLU cc_start: 0.8384 (tt0) cc_final: 0.8001 (mm-30) REVERT: A 441 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7677 (ttmt) REVERT: A 445 GLU cc_start: 0.6638 (pt0) cc_final: 0.6326 (pp20) REVERT: B 42 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8110 (mtpt) REVERT: B 106 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8332 (mm-30) REVERT: B 406 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8023 (mttt) REVERT: C 58 LYS cc_start: 0.7058 (mtpp) cc_final: 0.6824 (mttt) REVERT: C 95 LYS cc_start: 0.7421 (mtpp) cc_final: 0.6990 (mtpp) REVERT: C 106 LEU cc_start: 0.7100 (pt) cc_final: 0.5819 (tm) REVERT: C 149 MET cc_start: 0.8904 (mtm) cc_final: 0.8607 (mtm) REVERT: D 39 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: D 99 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7463 (mmpt) REVERT: D 159 LYS cc_start: 0.8810 (mtmm) cc_final: 0.8574 (mttt) REVERT: E 27 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8489 (p) REVERT: E 100 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7894 (tpt90) REVERT: F 82 LYS cc_start: 0.7509 (tttm) cc_final: 0.6854 (tmtt) REVERT: F 91 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6488 (tt) REVERT: F 214 MET cc_start: 0.6874 (mtm) cc_final: 0.6011 (mpp) REVERT: F 225 MET cc_start: 0.4590 (mtp) cc_final: 0.4317 (mmm) REVERT: F 245 MET cc_start: 0.3955 (tpp) cc_final: 0.3517 (tpp) REVERT: F 252 LEU cc_start: 0.6030 (mm) cc_final: 0.5228 (tt) REVERT: F 253 LYS cc_start: 0.4368 (mmtp) cc_final: 0.4012 (ptpp) REVERT: F 305 MET cc_start: 0.7656 (ptp) cc_final: 0.7255 (mtm) REVERT: F 309 TYR cc_start: 0.6931 (t80) cc_final: 0.6289 (t80) REVERT: F 317 MET cc_start: 0.7020 (ptp) cc_final: 0.6269 (mtm) REVERT: F 361 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6445 (mt-10) outliers start: 42 outliers final: 28 residues processed: 195 average time/residue: 0.6370 time to fit residues: 135.7492 Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 340 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 66 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 GLN E 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.180211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.144042 restraints weight = 12973.378| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.19 r_work: 0.3110 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15102 Z= 0.114 Angle : 0.529 12.462 20491 Z= 0.282 Chirality : 0.042 0.262 2322 Planarity : 0.005 0.053 2575 Dihedral : 6.498 106.388 2217 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.87 % Allowed : 16.26 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.66 (0.19), residues: 1888 helix: 1.58 (0.18), residues: 862 sheet: -0.10 (0.40), residues: 154 loop : -0.61 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 46 TYR 0.019 0.001 TYR D 141 PHE 0.047 0.001 PHE F 267 TRP 0.023 0.002 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (15097) covalent geometry : angle 0.52688 / 0.28 (20484) hydrogen bonds : bond 0.04360 / 2.92 ( 729) hydrogen bonds : angle 4.51906 / 3.18 ( 2043) metal coordination : bond 0.00405 / 0.22 ( 5) metal coordination : angle 2.81228 / 1.16 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5373.71 seconds wall clock time: 92 minutes 9.54 seconds (5529.54 seconds total)