Starting phenix.real_space_refine on Fri Mar 6 12:52:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a1u_15089/03_2026/8a1u_15089_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a1u_15089/03_2026/8a1u_15089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a1u_15089/03_2026/8a1u_15089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a1u_15089/03_2026/8a1u_15089.map" model { file = "/net/cci-nas-00/data/ceres_data/8a1u_15089/03_2026/8a1u_15089_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a1u_15089/03_2026/8a1u_15089_trim.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 P 10 5.49 5 S 90 5.16 5 Na 2 4.78 5 C 9773 2.51 5 N 2431 2.21 5 O 2948 1.98 5 H 14698 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29956 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6907 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 424} Chain: "B" Number of atoms: 6064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6064 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 14, 'TRANS': 380} Chain: "C" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 3814 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3173 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 9, 'TRANS': 192} Chain: "E" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3078 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "F" Number of atoms: 6232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6232 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 24, 'TRANS': 380} Chain: "B" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 287 Unusual residues: {' NA': 2, '3PE': 3, 'FMN': 1, 'LMT': 2, 'RBF': 1, 'UQ2': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'FAD': 1, 'FES': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18468 SG CYS D 112 67.470 82.093 58.748 1.00 62.30 S ATOM 20360 SG CYS E 26 64.820 82.419 61.324 1.00 45.30 S ATOM 17135 SG CYS D 29 68.048 84.324 64.922 1.00 49.86 S ATOM 21865 SG CYS E 120 70.928 84.246 62.438 1.00 49.97 S ATOM 24066 SG CYS F 70 51.840 65.779 37.331 1.00 25.59 S ATOM 24115 SG CYS F 76 50.749 62.207 36.894 1.00 16.87 S ATOM 24149 SG CYS F 79 55.484 60.490 38.329 1.00 17.24 S ATOM 24633 SG CYS F 111 56.705 64.001 38.884 1.00 19.42 S Time building chain proxies: 5.06, per 1000 atoms: 0.17 Number of scatterers: 29956 At special positions: 0 Unit cell: (114.57, 136.211, 132.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 4 26.01 S 90 16.00 P 10 15.00 Na 2 11.00 O 2948 8.00 N 2431 7.00 C 9773 6.00 H 14698 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 798.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1001 " pdb="FE1 FES E1001 " - pdb=" SG CYS E 26 " pdb="FE1 FES E1001 " - pdb=" SG CYS D 112 " pdb="FE2 FES E1001 " - pdb=" SG CYS E 120 " pdb="FE2 FES E1001 " - pdb=" SG CYS D 29 " pdb=" FES F1502 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " Number of angles added : 12 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 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: 91 helices and 14 sheets defined 54.8% alpha, 10.4% 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 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.601A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.632A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.775A pdb=" N LYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.597A 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 408 Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.608A pdb=" N GLU A 412 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 413' Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.627A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.696A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.777A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 152 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 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 243 Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.601A pdb=" N LEU B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 removed outlier: 3.541A pdb=" N ILE B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.616A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 8 through 54 removed outlier: 4.591A pdb=" N ASP C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.786A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 189 removed outlier: 3.793A pdb=" N TRP C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.597A pdb=" N ASP C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.773A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 93 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.647A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.647A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 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 202 removed outlier: 4.223A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 119 through 132 removed outlier: 3.763A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 3 through 30 Processing helix chain 'F' and resid 54 through 63 Processing helix chain 'F' and resid 91 through 96 Processing helix chain 'F' and resid 99 through 106 Processing helix chain 'F' and resid 124 through 130 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 185 through 195 removed outlier: 4.181A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 199 Processing helix chain 'F' and resid 243 through 251 Processing helix chain 'F' and resid 284 through 297 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 removed outlier: 3.530A pdb=" N ASN F 347 " --> pdb=" O PRO F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 369 through 373 Processing helix chain 'F' and resid 380 through 394 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 0 through 3 removed outlier: 6.193A pdb=" N HIS A 0 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP A 212 " --> pdb=" O HIS A 0 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 189 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N HIS A 209 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 191 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE A 211 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS A 193 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 removed outlier: 7.113A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.627A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.773A 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: 6.637A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.255A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 251 removed outlier: 3.551A pdb=" N GLN B 256 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 84 removed outlier: 4.133A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.188A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.398A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 169 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLU C 156 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N SER C 163 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA9, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'F' and resid 46 through 49 removed outlier: 6.486A pdb=" N THR F 36 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP F 120 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS F 82 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 224 through 229 Processing sheet with id=AB3, first strand: chain 'F' and resid 167 through 172 Processing sheet with id=AB4, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB5, first strand: chain 'F' and resid 351 through 352 removed outlier: 4.200A pdb=" N TYR F 351 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR F 309 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 768 hydrogen bonds defined for protein. 2169 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: 6.37 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 14685 1.11 - 1.39: 5896 1.39 - 1.66: 9375 1.66 - 1.93: 151 1.93 - 2.21: 8 Bond restraints: 30115 Sorted by residual: bond pdb=" C4 FMN C1000 " pdb=" C4A FMN C1000 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.389 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C4A FMN B 501 " pdb=" N5 FMN B 501 " ideal model delta sigma weight residual 1.300 1.376 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C4A FMN C1000 " pdb=" N5 FMN C1000 " ideal model delta sigma weight residual 1.300 1.375 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 RBF B 502 " pdb=" C4A RBF B 502 " ideal model delta sigma weight residual 1.481 1.406 0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 30110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 53990 1.92 - 3.83: 273 3.83 - 5.75: 61 5.75 - 7.67: 9 7.67 - 9.59: 9 Bond angle restraints: 54342 Sorted by residual: angle pdb=" C2 LMT B 503 " pdb=" C3 LMT B 503 " pdb=" C4 LMT B 503 " ideal model delta sigma weight residual 117.09 107.50 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C2 LMT B 505 " pdb=" C3 LMT B 505 " pdb=" C4 LMT B 505 " ideal model delta sigma weight residual 117.09 107.72 9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" C2 LMT D 302 " pdb=" C3 LMT D 302 " pdb=" C4 LMT D 302 " ideal model delta sigma weight residual 117.09 107.76 9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" C10 LMT B 505 " pdb=" C9 LMT B 505 " pdb=" C8 LMT B 505 " ideal model delta sigma weight residual 116.03 107.48 8.55 3.00e+00 1.11e-01 8.12e+00 angle pdb=" C10 LMT B 503 " pdb=" C9 LMT B 503 " pdb=" C8 LMT B 503 " ideal model delta sigma weight residual 116.03 107.76 8.27 3.00e+00 1.11e-01 7.60e+00 ... (remaining 54337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.33: 13424 25.33 - 50.66: 731 50.66 - 75.99: 209 75.99 - 101.32: 33 101.32 - 126.65: 11 Dihedral angle restraints: 14408 sinusoidal: 7993 harmonic: 6415 Sorted by residual: dihedral pdb=" O5' FAD F1501 " pdb=" O3P FAD F1501 " pdb=" P FAD F1501 " pdb=" PA FAD F1501 " ideal model delta sinusoidal sigma weight residual 298.23 171.58 126.65 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C1B LMT D 302 " pdb=" C5B LMT D 302 " pdb=" O5B LMT D 302 " pdb=" C6B LMT D 302 " ideal model delta sinusoidal sigma weight residual 175.31 -59.75 -124.94 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C1B LMT D 302 " pdb=" C5B LMT D 302 " pdb=" O5B LMT D 302 " pdb=" C4B LMT D 302 " ideal model delta sinusoidal sigma weight residual -59.84 64.71 -124.55 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 14405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1905 0.045 - 0.091: 306 0.091 - 0.136: 124 0.136 - 0.181: 3 0.181 - 0.226: 11 Chirality restraints: 2349 Sorted by residual: chirality pdb=" C4' LMT D 302 " pdb=" C3' LMT D 302 " pdb=" C5' LMT D 302 " pdb=" O1B LMT D 302 " both_signs ideal model delta sigma weight residual False -2.55 -2.78 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C4' LMT B 505 " pdb=" C3' LMT B 505 " pdb=" C5' LMT B 505 " pdb=" O1B LMT B 505 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C4' LMT B 503 " pdb=" C3' LMT B 503 " pdb=" C5' LMT B 503 " pdb=" O1B LMT B 503 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2346 not shown) Planarity restraints: 4397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ2 B 507 " 0.004 2.00e-02 2.50e+03 3.27e-02 3.20e+01 pdb=" C2 UQ2 B 507 " 0.020 2.00e-02 2.50e+03 pdb=" C3 UQ2 B 507 " -0.019 2.00e-02 2.50e+03 pdb=" C4 UQ2 B 507 " -0.000 2.00e-02 2.50e+03 pdb=" C5 UQ2 B 507 " 0.022 2.00e-02 2.50e+03 pdb=" C6 UQ2 B 507 " -0.009 2.00e-02 2.50e+03 pdb=" C7 UQ2 B 507 " -0.057 2.00e-02 2.50e+03 pdb=" CM5 UQ2 B 507 " 0.049 2.00e-02 2.50e+03 pdb=" O1 UQ2 B 507 " -0.003 2.00e-02 2.50e+03 pdb=" O2 UQ2 B 507 " 0.052 2.00e-02 2.50e+03 pdb=" O3 UQ2 B 507 " -0.055 2.00e-02 2.50e+03 pdb=" O4 UQ2 B 507 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 128 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO D 129 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 129 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 129 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 206 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO F 207 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 207 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 207 " -0.018 5.00e-02 4.00e+02 ... (remaining 4394 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 1054 2.16 - 2.77: 57820 2.77 - 3.38: 87399 3.38 - 3.99: 114794 3.99 - 4.60: 178842 Nonbonded interactions: 439909 Sorted by model distance: nonbonded pdb=" O LYS E 10 " pdb=" H GLU E 15 " model vdw 1.556 2.450 nonbonded pdb=" O GLY E 175 " pdb=" HG1 THR E 179 " model vdw 1.563 2.450 nonbonded pdb=" O PHE A 351 " pdb=" HD1 HIS A 354 " model vdw 1.643 2.450 nonbonded pdb=" H GLY B 198 " pdb=" O5' RBF B 502 " model vdw 1.649 2.450 nonbonded pdb=" HH TYR B 360 " pdb=" OD1 ASN B 390 " model vdw 1.652 2.450 ... (remaining 439904 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 32.820 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 : 0.004 0.097 15427 Z= 0.214 Angle : 0.582 9.586 20899 Z= 0.260 Chirality : 0.042 0.226 2349 Planarity : 0.003 0.037 2589 Dihedral : 17.625 126.648 5849 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.71 % Allowed : 12.90 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.20), residues: 1886 helix: 2.50 (0.18), residues: 881 sheet: 0.11 (0.39), residues: 173 loop : 0.22 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 436 TYR 0.013 0.001 TYR B 360 PHE 0.011 0.001 PHE B 213 TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00415 (15417) covalent geometry : angle 0.58046 (20887) hydrogen bonds : bond 0.05256 ( 768) hydrogen bonds : angle 4.31389 ( 2169) metal coordination : bond 0.01234 ( 8) metal coordination : angle 1.75258 ( 12) Misc. bond : bond 0.04514 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 227 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8282 (mt-10) REVERT: A 292 MET cc_start: 0.7909 (mtt) cc_final: 0.7692 (mtm) REVERT: A 374 MET cc_start: 0.8788 (ttt) cc_final: 0.8501 (ttt) REVERT: A 433 GLN cc_start: 0.7974 (tp40) cc_final: 0.7690 (tp-100) REVERT: A 441 LYS cc_start: 0.7733 (tttt) cc_final: 0.7499 (ttmp) REVERT: A 445 GLU cc_start: 0.7402 (tt0) cc_final: 0.6834 (tp30) REVERT: B 154 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6541 (mm-30) REVERT: C 118 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7651 (ttp80) REVERT: C 125 TYR cc_start: 0.8926 (m-80) cc_final: 0.8645 (m-80) REVERT: D 44 MET cc_start: 0.8884 (tpt) cc_final: 0.8578 (tpt) REVERT: D 63 ARG cc_start: 0.7346 (ptt-90) cc_final: 0.7058 (ptt90) REVERT: D 124 LYS cc_start: 0.7821 (pttt) cc_final: 0.7573 (ptpp) REVERT: D 159 LYS cc_start: 0.8587 (mtmt) cc_final: 0.7999 (mtmt) REVERT: E 36 LYS cc_start: 0.6971 (ptmm) cc_final: 0.6770 (ptmm) REVERT: E 57 ASN cc_start: 0.6884 (t0) cc_final: 0.6659 (t0) REVERT: F 10 MET cc_start: 0.5992 (tpp) cc_final: 0.5779 (tpp) REVERT: F 21 VAL cc_start: 0.6815 (t) cc_final: 0.6605 (p) REVERT: F 115 VAL cc_start: 0.6905 (p) cc_final: 0.6700 (p) outliers start: 11 outliers final: 12 residues processed: 238 average time/residue: 1.2418 time to fit residues: 327.2429 Evaluate side-chains 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 183 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 HIS C 257 ASN D 68 ASN E 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.163819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.114035 restraints weight = 46193.279| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.53 r_work: 0.2938 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15427 Z= 0.157 Angle : 0.519 7.546 20899 Z= 0.258 Chirality : 0.042 0.187 2349 Planarity : 0.004 0.046 2589 Dihedral : 12.673 130.304 2536 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.35 % Allowed : 17.10 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1886 helix: 2.24 (0.18), residues: 881 sheet: 0.00 (0.39), residues: 175 loop : 0.07 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.012 0.001 TYR B 360 PHE 0.016 0.001 PHE B 392 TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00362 (15417) covalent geometry : angle 0.51179 (20887) hydrogen bonds : bond 0.04178 ( 768) hydrogen bonds : angle 4.34196 ( 2169) metal coordination : bond 0.00863 ( 8) metal coordination : angle 3.58840 ( 12) Misc. bond : bond 0.00223 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7890 (ttp) cc_final: 0.7677 (tpp) REVERT: A 40 ARG cc_start: 0.7990 (mmp80) cc_final: 0.7568 (mmp80) REVERT: A 292 MET cc_start: 0.7996 (mtt) cc_final: 0.7791 (mtm) REVERT: A 374 MET cc_start: 0.8992 (ttt) cc_final: 0.8560 (ttt) REVERT: A 388 MET cc_start: 0.9230 (mtt) cc_final: 0.8856 (mtp) REVERT: A 433 GLN cc_start: 0.8159 (tp40) cc_final: 0.7917 (tp-100) REVERT: A 441 LYS cc_start: 0.8052 (tttt) cc_final: 0.7821 (ttmp) REVERT: A 445 GLU cc_start: 0.7727 (tt0) cc_final: 0.6824 (tp30) REVERT: B 154 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6846 (mm-30) REVERT: C 118 ARG cc_start: 0.7792 (ttp-170) cc_final: 0.7538 (ttp80) REVERT: C 125 TYR cc_start: 0.8980 (m-80) cc_final: 0.8636 (m-80) REVERT: D 44 MET cc_start: 0.8963 (tpt) cc_final: 0.8565 (tpt) REVERT: D 124 LYS cc_start: 0.7647 (pttt) cc_final: 0.7435 (ptpp) REVERT: D 159 LYS cc_start: 0.8496 (mtmt) cc_final: 0.7951 (mtmt) REVERT: E 57 ASN cc_start: 0.6750 (t0) cc_final: 0.6543 (t0) REVERT: E 105 LEU cc_start: 0.5663 (mm) cc_final: 0.5248 (mt) REVERT: F 115 VAL cc_start: 0.6614 (p) cc_final: 0.6381 (p) REVERT: F 245 MET cc_start: 0.5437 (tpp) cc_final: 0.5177 (tpp) REVERT: F 266 GLU cc_start: 0.6109 (mm-30) cc_final: 0.5902 (mm-30) outliers start: 21 outliers final: 17 residues processed: 214 average time/residue: 1.2047 time to fit residues: 285.2320 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 39 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 HIS D 68 ASN D 75 GLN E 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.162582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112948 restraints weight = 45921.060| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.50 r_work: 0.2891 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15427 Z= 0.217 Angle : 0.580 9.310 20899 Z= 0.289 Chirality : 0.044 0.269 2349 Planarity : 0.005 0.065 2589 Dihedral : 11.283 131.789 2530 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.00 % Allowed : 16.65 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 1886 helix: 1.81 (0.18), residues: 880 sheet: -0.08 (0.38), residues: 170 loop : -0.19 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 108 TYR 0.014 0.002 TYR F 179 PHE 0.021 0.002 PHE B 159 TRP 0.019 0.002 TRP B 103 HIS 0.008 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00510 (15417) covalent geometry : angle 0.57031 (20887) hydrogen bonds : bond 0.04825 ( 768) hydrogen bonds : angle 4.58764 ( 2169) metal coordination : bond 0.01098 ( 8) metal coordination : angle 4.39163 ( 12) Misc. bond : bond 0.00230 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8045 (mmp80) cc_final: 0.7624 (mmp80) REVERT: A 292 MET cc_start: 0.8086 (mtt) cc_final: 0.7820 (mtm) REVERT: A 339 MET cc_start: 0.8474 (mmm) cc_final: 0.8247 (mmt) REVERT: A 374 MET cc_start: 0.9054 (ttt) cc_final: 0.8679 (ttt) REVERT: A 388 MET cc_start: 0.9399 (mtt) cc_final: 0.9028 (mtt) REVERT: A 445 GLU cc_start: 0.7828 (tt0) cc_final: 0.6952 (tp30) REVERT: B 154 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6901 (mm-30) REVERT: B 256 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8590 (mt0) REVERT: B 346 ASP cc_start: 0.8759 (t0) cc_final: 0.8479 (t0) REVERT: C 118 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7441 (ttp80) REVERT: C 125 TYR cc_start: 0.9024 (m-80) cc_final: 0.8686 (m-80) REVERT: D 124 LYS cc_start: 0.7740 (pttt) cc_final: 0.7497 (ptpp) REVERT: D 159 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8052 (mtmt) REVERT: E 57 ASN cc_start: 0.6803 (t0) cc_final: 0.6527 (t0) REVERT: E 105 LEU cc_start: 0.5860 (mm) cc_final: 0.5440 (mt) REVERT: E 106 TYR cc_start: 0.5646 (t80) cc_final: 0.5201 (t80) REVERT: F 105 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5948 (mt-10) REVERT: F 245 MET cc_start: 0.5380 (tpp) cc_final: 0.5154 (tpp) REVERT: F 266 GLU cc_start: 0.6136 (mm-30) cc_final: 0.5892 (mm-30) outliers start: 31 outliers final: 19 residues processed: 216 average time/residue: 1.2032 time to fit residues: 289.1035 Evaluate side-chains 205 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 57 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 107 ASN F 362 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.159283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108127 restraints weight = 45689.191| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.43 r_work: 0.2896 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15427 Z= 0.231 Angle : 0.588 9.813 20899 Z= 0.296 Chirality : 0.044 0.299 2349 Planarity : 0.005 0.064 2589 Dihedral : 10.802 133.502 2530 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.26 % Allowed : 17.55 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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: 0.78 (0.19), residues: 1886 helix: 1.55 (0.18), residues: 879 sheet: -0.27 (0.38), residues: 170 loop : -0.37 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 229 TYR 0.017 0.002 TYR F 179 PHE 0.020 0.002 PHE B 159 TRP 0.020 0.002 TRP B 103 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00544 (15417) covalent geometry : angle 0.57670 (20887) hydrogen bonds : bond 0.04929 ( 768) hydrogen bonds : angle 4.67872 ( 2169) metal coordination : bond 0.01263 ( 8) metal coordination : angle 4.83393 ( 12) Misc. bond : bond 0.00249 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8087 (mtt) cc_final: 0.7853 (mtm) REVERT: A 339 MET cc_start: 0.8482 (mmm) cc_final: 0.8260 (mmt) REVERT: A 374 MET cc_start: 0.9075 (ttt) cc_final: 0.8716 (ttt) REVERT: A 388 MET cc_start: 0.9410 (mtt) cc_final: 0.9043 (mtt) REVERT: A 445 GLU cc_start: 0.7973 (tt0) cc_final: 0.7052 (tp30) REVERT: B 20 HIS cc_start: 0.2527 (OUTLIER) cc_final: 0.2269 (t-170) REVERT: B 154 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6846 (tp30) REVERT: B 256 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8570 (mt0) REVERT: C 118 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7489 (ttp80) REVERT: C 149 MET cc_start: 0.9080 (mtp) cc_final: 0.8646 (mtp) REVERT: D 124 LYS cc_start: 0.7744 (pttt) cc_final: 0.7505 (ptpp) REVERT: D 159 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8044 (mtmt) REVERT: E 105 LEU cc_start: 0.5850 (mm) cc_final: 0.5434 (mt) REVERT: F 21 VAL cc_start: 0.7320 (OUTLIER) cc_final: 0.7064 (p) REVERT: F 105 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6012 (mt-10) REVERT: F 245 MET cc_start: 0.5315 (tpp) cc_final: 0.5079 (tpp) REVERT: F 266 GLU cc_start: 0.6156 (mm-30) cc_final: 0.5900 (mm-30) outliers start: 35 outliers final: 20 residues processed: 214 average time/residue: 1.1591 time to fit residues: 277.6073 Evaluate side-chains 211 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 318 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 36 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 chunk 118 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.162669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112082 restraints weight = 45828.661| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.49 r_work: 0.2889 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15427 Z= 0.164 Angle : 0.538 10.266 20899 Z= 0.270 Chirality : 0.042 0.317 2349 Planarity : 0.004 0.057 2589 Dihedral : 10.288 132.015 2529 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.19 % Allowed : 18.26 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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: 0.85 (0.19), residues: 1886 helix: 1.66 (0.18), residues: 879 sheet: -0.27 (0.38), residues: 172 loop : -0.38 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.019 0.001 TYR F 179 PHE 0.017 0.001 PHE B 159 TRP 0.019 0.001 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00378 (15417) covalent geometry : angle 0.52681 (20887) hydrogen bonds : bond 0.04509 ( 768) hydrogen bonds : angle 4.58027 ( 2169) metal coordination : bond 0.01018 ( 8) metal coordination : angle 4.63061 ( 12) Misc. bond : bond 0.00165 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8086 (mtt) cc_final: 0.7835 (mtm) REVERT: A 374 MET cc_start: 0.9042 (ttt) cc_final: 0.8663 (ttt) REVERT: A 388 MET cc_start: 0.9413 (mtt) cc_final: 0.9035 (mtt) REVERT: A 445 GLU cc_start: 0.7980 (tt0) cc_final: 0.7075 (tp30) REVERT: B 20 HIS cc_start: 0.2529 (OUTLIER) cc_final: 0.2244 (t-90) REVERT: B 154 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6836 (tp30) REVERT: B 256 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8584 (mt0) REVERT: C 118 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7493 (ttp80) REVERT: C 125 TYR cc_start: 0.8963 (m-80) cc_final: 0.8665 (m-80) REVERT: C 149 MET cc_start: 0.9154 (mtp) cc_final: 0.8799 (mtp) REVERT: D 124 LYS cc_start: 0.7736 (pttt) cc_final: 0.7506 (ptpp) REVERT: D 159 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8031 (mtmt) REVERT: E 105 LEU cc_start: 0.5817 (mm) cc_final: 0.5411 (mt) REVERT: F 21 VAL cc_start: 0.7293 (OUTLIER) cc_final: 0.7045 (p) REVERT: F 105 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6031 (mt-10) REVERT: F 245 MET cc_start: 0.5314 (tpp) cc_final: 0.5040 (tpp) REVERT: F 266 GLU cc_start: 0.6189 (mm-30) cc_final: 0.5902 (mm-30) outliers start: 34 outliers final: 21 residues processed: 214 average time/residue: 1.1371 time to fit residues: 272.2874 Evaluate side-chains 215 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 318 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 51 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.159810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.106237 restraints weight = 45816.649| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.58 r_work: 0.2832 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15427 Z= 0.218 Angle : 0.575 10.113 20899 Z= 0.291 Chirality : 0.044 0.297 2349 Planarity : 0.005 0.069 2589 Dihedral : 10.318 132.886 2527 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.58 % Allowed : 17.81 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1886 helix: 1.50 (0.18), residues: 879 sheet: -0.38 (0.37), residues: 172 loop : -0.47 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 372 TYR 0.022 0.002 TYR F 179 PHE 0.020 0.002 PHE B 392 TRP 0.020 0.002 TRP B 103 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00512 (15417) covalent geometry : angle 0.56309 (20887) hydrogen bonds : bond 0.04864 ( 768) hydrogen bonds : angle 4.67128 ( 2169) metal coordination : bond 0.01193 ( 8) metal coordination : angle 4.81409 ( 12) Misc. bond : bond 0.00229 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8053 (mtt) cc_final: 0.7842 (mtm) REVERT: A 374 MET cc_start: 0.9055 (ttt) cc_final: 0.8713 (ttt) REVERT: A 388 MET cc_start: 0.9373 (mtt) cc_final: 0.9017 (mtt) REVERT: A 445 GLU cc_start: 0.7954 (tt0) cc_final: 0.6982 (tp30) REVERT: B 20 HIS cc_start: 0.2452 (OUTLIER) cc_final: 0.2125 (t-90) REVERT: B 154 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6811 (mm-30) REVERT: B 256 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8610 (mt0) REVERT: C 118 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7465 (ttp80) REVERT: C 125 TYR cc_start: 0.8974 (m-80) cc_final: 0.8635 (m-80) REVERT: C 149 MET cc_start: 0.9075 (mtp) cc_final: 0.8681 (mtp) REVERT: C 156 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: D 124 LYS cc_start: 0.7639 (pttt) cc_final: 0.7433 (ptpp) REVERT: D 145 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7401 (mp) REVERT: D 159 LYS cc_start: 0.8540 (mtmt) cc_final: 0.7974 (mtmt) REVERT: E 105 LEU cc_start: 0.5592 (mm) cc_final: 0.5233 (mt) REVERT: F 21 VAL cc_start: 0.7188 (OUTLIER) cc_final: 0.6955 (p) REVERT: F 102 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6273 (mm-30) REVERT: F 105 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5895 (mt-10) REVERT: F 266 GLU cc_start: 0.6161 (mm-30) cc_final: 0.5852 (mm-30) outliers start: 40 outliers final: 24 residues processed: 219 average time/residue: 1.1324 time to fit residues: 278.2757 Evaluate side-chains 218 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 318 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 127 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.160932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110183 restraints weight = 45609.316| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.51 r_work: 0.2929 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15427 Z= 0.128 Angle : 0.514 10.319 20899 Z= 0.258 Chirality : 0.041 0.286 2349 Planarity : 0.004 0.058 2589 Dihedral : 9.866 130.497 2527 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.39 % Allowed : 17.94 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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: 0.89 (0.19), residues: 1886 helix: 1.72 (0.18), residues: 879 sheet: -0.30 (0.38), residues: 172 loop : -0.38 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 349 TYR 0.020 0.001 TYR F 179 PHE 0.015 0.001 PHE B 159 TRP 0.019 0.001 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00289 (15417) covalent geometry : angle 0.50270 (20887) hydrogen bonds : bond 0.04216 ( 768) hydrogen bonds : angle 4.52053 ( 2169) metal coordination : bond 0.00896 ( 8) metal coordination : angle 4.51492 ( 12) Misc. bond : bond 0.00105 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8035 (mtt) cc_final: 0.7787 (mtm) REVERT: A 374 MET cc_start: 0.8981 (ttt) cc_final: 0.8488 (ttt) REVERT: A 388 MET cc_start: 0.9399 (mtt) cc_final: 0.9030 (mtt) REVERT: A 404 SER cc_start: 0.8739 (t) cc_final: 0.8461 (t) REVERT: A 445 GLU cc_start: 0.7914 (tt0) cc_final: 0.7025 (tp30) REVERT: B 20 HIS cc_start: 0.2516 (OUTLIER) cc_final: 0.2204 (t-90) REVERT: B 256 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8584 (mt0) REVERT: C 90 ASN cc_start: 0.7495 (p0) cc_final: 0.7178 (m-40) REVERT: C 110 GLN cc_start: 0.7297 (mt0) cc_final: 0.6890 (mt0) REVERT: C 125 TYR cc_start: 0.8925 (m-80) cc_final: 0.8624 (m-80) REVERT: C 149 MET cc_start: 0.9125 (mtp) cc_final: 0.8655 (mtp) REVERT: C 156 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: D 124 LYS cc_start: 0.7457 (pttt) cc_final: 0.7251 (ptpp) REVERT: D 159 LYS cc_start: 0.8491 (mtmt) cc_final: 0.7875 (mtmt) REVERT: E 105 LEU cc_start: 0.5627 (mm) cc_final: 0.5251 (mt) REVERT: F 21 VAL cc_start: 0.7257 (OUTLIER) cc_final: 0.7023 (p) REVERT: F 102 GLU cc_start: 0.6524 (mm-30) cc_final: 0.6318 (mm-30) REVERT: F 105 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5946 (mt-10) REVERT: F 247 SER cc_start: 0.5031 (m) cc_final: 0.4696 (p) REVERT: F 266 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5905 (mm-30) outliers start: 37 outliers final: 23 residues processed: 220 average time/residue: 1.1344 time to fit residues: 279.3441 Evaluate side-chains 218 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 173 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 120 optimal weight: 0.0270 chunk 13 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 142 ASN F 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.161255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.111106 restraints weight = 45949.239| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.48 r_work: 0.2924 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15427 Z= 0.121 Angle : 0.507 9.915 20899 Z= 0.254 Chirality : 0.041 0.270 2349 Planarity : 0.004 0.061 2589 Dihedral : 9.565 128.507 2527 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.81 % Allowed : 18.65 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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: 0.98 (0.19), residues: 1886 helix: 1.78 (0.18), residues: 886 sheet: -0.26 (0.38), residues: 172 loop : -0.35 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 349 TYR 0.021 0.001 TYR F 179 PHE 0.014 0.001 PHE B 159 TRP 0.019 0.001 TRP B 103 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00273 (15417) covalent geometry : angle 0.49631 (20887) hydrogen bonds : bond 0.04052 ( 768) hydrogen bonds : angle 4.44580 ( 2169) metal coordination : bond 0.00794 ( 8) metal coordination : angle 4.28893 ( 12) Misc. bond : bond 0.00088 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8054 (mtt) cc_final: 0.7789 (mtm) REVERT: A 374 MET cc_start: 0.8989 (ttt) cc_final: 0.8500 (ttt) REVERT: A 388 MET cc_start: 0.9401 (mtt) cc_final: 0.9062 (mtt) REVERT: A 396 ASP cc_start: 0.7781 (m-30) cc_final: 0.7528 (m-30) REVERT: A 404 SER cc_start: 0.8671 (t) cc_final: 0.8471 (t) REVERT: A 445 GLU cc_start: 0.7961 (tt0) cc_final: 0.7098 (tp30) REVERT: B 20 HIS cc_start: 0.2512 (OUTLIER) cc_final: 0.2204 (t-90) REVERT: B 256 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8562 (mt0) REVERT: C 110 GLN cc_start: 0.7282 (mt0) cc_final: 0.6824 (mt0) REVERT: C 125 TYR cc_start: 0.8958 (m-80) cc_final: 0.8669 (m-80) REVERT: C 149 MET cc_start: 0.9146 (mtp) cc_final: 0.8727 (mtp) REVERT: D 159 LYS cc_start: 0.8554 (mtmt) cc_final: 0.7963 (mtmt) REVERT: E 105 LEU cc_start: 0.5656 (mm) cc_final: 0.5271 (mt) REVERT: F 21 VAL cc_start: 0.7296 (OUTLIER) cc_final: 0.7095 (p) REVERT: F 105 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5806 (mt-10) REVERT: F 182 PHE cc_start: 0.1837 (m-10) cc_final: 0.1605 (m-10) REVERT: F 247 SER cc_start: 0.5000 (m) cc_final: 0.4720 (p) REVERT: F 266 GLU cc_start: 0.5853 (mm-30) cc_final: 0.5531 (mm-30) REVERT: F 295 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.6586 (mp10) outliers start: 28 outliers final: 22 residues processed: 208 average time/residue: 1.1384 time to fit residues: 265.4250 Evaluate side-chains 212 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 318 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 1 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN F 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.163062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.114406 restraints weight = 45791.921| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.56 r_work: 0.2957 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15427 Z= 0.096 Angle : 0.481 9.072 20899 Z= 0.241 Chirality : 0.040 0.256 2349 Planarity : 0.004 0.059 2589 Dihedral : 9.027 125.671 2525 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.61 % Allowed : 19.03 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 1886 helix: 1.96 (0.18), residues: 887 sheet: -0.14 (0.38), residues: 170 loop : -0.28 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 349 TYR 0.020 0.001 TYR F 179 PHE 0.012 0.001 PHE B 159 TRP 0.019 0.001 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00206 (15417) covalent geometry : angle 0.47178 (20887) hydrogen bonds : bond 0.03642 ( 768) hydrogen bonds : angle 4.30280 ( 2169) metal coordination : bond 0.00625 ( 8) metal coordination : angle 4.00738 ( 12) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 MET cc_start: 0.8936 (ttt) cc_final: 0.8438 (ttt) REVERT: A 388 MET cc_start: 0.9381 (mtt) cc_final: 0.9020 (mtt) REVERT: A 403 ASP cc_start: 0.8609 (m-30) cc_final: 0.8176 (m-30) REVERT: A 445 GLU cc_start: 0.7743 (tt0) cc_final: 0.6904 (tp30) REVERT: B 20 HIS cc_start: 0.2505 (OUTLIER) cc_final: 0.2123 (t-90) REVERT: B 256 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8564 (mt0) REVERT: C 110 GLN cc_start: 0.7220 (mt0) cc_final: 0.6759 (mt0) REVERT: C 125 TYR cc_start: 0.8931 (m-80) cc_final: 0.8600 (m-80) REVERT: C 149 MET cc_start: 0.9145 (mtp) cc_final: 0.8791 (mtp) REVERT: D 124 LYS cc_start: 0.6969 (ptpp) cc_final: 0.6716 (pttt) REVERT: D 159 LYS cc_start: 0.8496 (mtmt) cc_final: 0.7932 (mtmt) REVERT: E 105 LEU cc_start: 0.5542 (mm) cc_final: 0.5158 (mt) REVERT: F 105 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5797 (mt-10) REVERT: F 247 SER cc_start: 0.5011 (m) cc_final: 0.4717 (p) REVERT: F 266 GLU cc_start: 0.5873 (mm-30) cc_final: 0.5626 (mm-30) REVERT: F 295 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6394 (mp10) outliers start: 25 outliers final: 17 residues processed: 201 average time/residue: 1.1606 time to fit residues: 261.2276 Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 318 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 185 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 180 optimal weight: 0.0000 chunk 154 optimal weight: 0.0050 chunk 24 optimal weight: 2.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.161315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112017 restraints weight = 46027.381| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.64 r_work: 0.2934 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15427 Z= 0.107 Angle : 0.494 8.904 20899 Z= 0.247 Chirality : 0.040 0.246 2349 Planarity : 0.004 0.057 2589 Dihedral : 8.940 125.383 2523 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.29 % Allowed : 19.48 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 1886 helix: 1.97 (0.18), residues: 887 sheet: -0.11 (0.38), residues: 170 loop : -0.27 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 349 TYR 0.038 0.001 TYR F 179 PHE 0.029 0.001 PHE F 182 TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00242 (15417) covalent geometry : angle 0.48432 (20887) hydrogen bonds : bond 0.03744 ( 768) hydrogen bonds : angle 4.29020 ( 2169) metal coordination : bond 0.00714 ( 8) metal coordination : angle 4.00275 ( 12) Misc. bond : bond 0.00069 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 MET cc_start: 0.8978 (ttt) cc_final: 0.8512 (ttt) REVERT: A 388 MET cc_start: 0.9423 (mtt) cc_final: 0.9076 (mtt) REVERT: A 403 ASP cc_start: 0.8765 (m-30) cc_final: 0.8350 (m-30) REVERT: A 445 GLU cc_start: 0.7917 (tt0) cc_final: 0.7085 (tp30) REVERT: B 20 HIS cc_start: 0.2554 (OUTLIER) cc_final: 0.2178 (t-90) REVERT: B 256 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8578 (mt0) REVERT: C 110 GLN cc_start: 0.7257 (mt0) cc_final: 0.6774 (mt0) REVERT: C 125 TYR cc_start: 0.9010 (m-80) cc_final: 0.8690 (m-80) REVERT: C 149 MET cc_start: 0.9192 (mtp) cc_final: 0.8850 (mtp) REVERT: D 124 LYS cc_start: 0.7101 (ptpp) cc_final: 0.6871 (pttt) REVERT: D 159 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8053 (mtmt) REVERT: E 105 LEU cc_start: 0.5673 (mm) cc_final: 0.5295 (mt) REVERT: F 105 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5827 (mt-10) REVERT: F 247 SER cc_start: 0.4702 (m) cc_final: 0.4478 (p) REVERT: F 266 GLU cc_start: 0.5969 (mm-30) cc_final: 0.5613 (mm-30) outliers start: 20 outliers final: 17 residues processed: 195 average time/residue: 1.1976 time to fit residues: 261.3212 Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 318 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 64 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.160850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110212 restraints weight = 46003.077| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.43 r_work: 0.2924 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15427 Z= 0.147 Angle : 0.524 8.938 20899 Z= 0.263 Chirality : 0.041 0.247 2349 Planarity : 0.004 0.059 2589 Dihedral : 9.136 126.576 2523 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 19.42 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 1886 helix: 1.88 (0.18), residues: 886 sheet: -0.24 (0.38), residues: 172 loop : -0.31 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 349 TYR 0.038 0.001 TYR F 179 PHE 0.040 0.001 PHE F 182 TRP 0.019 0.001 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00340 (15417) covalent geometry : angle 0.51544 (20887) hydrogen bonds : bond 0.04117 ( 768) hydrogen bonds : angle 4.39469 ( 2169) metal coordination : bond 0.00827 ( 8) metal coordination : angle 4.06102 ( 12) Misc. bond : bond 0.00136 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10154.83 seconds wall clock time: 172 minutes 4.45 seconds (10324.45 seconds total)