Starting phenix.real_space_refine on Fri Jun 5 01:58:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wq3_66158/06_2026/9wq3_66158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wq3_66158/06_2026/9wq3_66158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wq3_66158/06_2026/9wq3_66158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wq3_66158/06_2026/9wq3_66158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wq3_66158/06_2026/9wq3_66158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wq3_66158/06_2026/9wq3_66158.map" } resolution = 3.27 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= 0.004 sd= 0.084 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 12 5.16 5 C 10669 2.51 5 N 2793 2.21 5 O 3133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16619 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2711 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 9, 'TRANS': 327} Chain: "B" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2729 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain: "D" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2729 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2729 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain: "F" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2729 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain: "G" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2722 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 9, 'TRANS': 328} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.68, per 1000 atoms: 0.28 Number of scatterers: 16619 At special positions: 0 Unit cell: (130, 101.92, 133.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 12 15.00 O 3133 8.00 N 2793 7.00 C 10669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 802.7 milliseconds 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3834 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 13 sheets defined 47.3% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 removed outlier: 3.562A pdb=" N PHE A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 69 Processing helix chain 'A' and resid 70 through 76 removed outlier: 3.586A pdb=" N LEU A 76 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 106 Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.839A pdb=" N LEU A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 153 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 158 through 177 Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.971A pdb=" N SER A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.544A pdb=" N SER A 264 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN A 265 " --> pdb=" O ASP A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 288 through 309 removed outlier: 3.739A pdb=" N ASN A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'B' and resid 33 through 50 removed outlier: 3.742A pdb=" N PHE B 37 " --> pdb=" O GLY B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 69 Processing helix chain 'B' and resid 83 through 104 Processing helix chain 'B' and resid 142 through 153 Processing helix chain 'B' and resid 158 through 177 Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.843A pdb=" N THR B 243 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 309 removed outlier: 3.515A pdb=" N ASN B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.981A pdb=" N PHE B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 49 removed outlier: 4.476A pdb=" N SER D 39 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 69 Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.977A pdb=" N LYS D 74 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 104 Processing helix chain 'D' and resid 142 through 153 Processing helix chain 'D' and resid 154 through 177 Proline residue: D 160 - end of helix removed outlier: 3.547A pdb=" N GLU D 171 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 236 through 241 removed outlier: 3.854A pdb=" N LEU D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 236 through 241' Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 287 through 309 removed outlier: 3.733A pdb=" N ASN D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 358 through 362 removed outlier: 3.799A pdb=" N ASN D 361 " --> pdb=" O ASN D 358 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS D 362 " --> pdb=" O LYS D 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 358 through 362' Processing helix chain 'E' and resid 33 through 49 removed outlier: 3.910A pdb=" N PHE E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 69 Processing helix chain 'E' and resid 70 through 76 removed outlier: 4.315A pdb=" N LYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 104 Processing helix chain 'E' and resid 142 through 153 Processing helix chain 'E' and resid 154 through 157 removed outlier: 3.502A pdb=" N ASN E 157 " --> pdb=" O THR E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 154 through 157' Processing helix chain 'E' and resid 158 through 177 removed outlier: 3.595A pdb=" N PHE E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU E 171 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'E' and resid 236 through 241 Processing helix chain 'E' and resid 259 through 265 removed outlier: 3.682A pdb=" N THR E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN E 265 " --> pdb=" O HIS E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 309 removed outlier: 3.771A pdb=" N ASN E 309 " --> pdb=" O ILE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'F' and resid 33 through 49 Processing helix chain 'F' and resid 51 through 69 Processing helix chain 'F' and resid 70 through 76 removed outlier: 3.926A pdb=" N LEU F 76 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 106 Processing helix chain 'F' and resid 121 through 125 removed outlier: 3.795A pdb=" N GLN F 125 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 153 removed outlier: 3.544A pdb=" N LYS F 148 " --> pdb=" O LYS F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 157 removed outlier: 3.546A pdb=" N ASN F 157 " --> pdb=" O THR F 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 157' Processing helix chain 'F' and resid 158 through 177 Processing helix chain 'F' and resid 189 through 199 Processing helix chain 'F' and resid 238 through 243 removed outlier: 3.944A pdb=" N SER F 242 " --> pdb=" O GLN F 238 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 238 through 243' Processing helix chain 'F' and resid 287 through 309 removed outlier: 3.511A pdb=" N ASN F 309 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 358 through 362 removed outlier: 4.030A pdb=" N ASN F 361 " --> pdb=" O ASN F 358 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS F 362 " --> pdb=" O LYS F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 362' Processing helix chain 'G' and resid 33 through 49 Processing helix chain 'G' and resid 51 through 69 removed outlier: 3.511A pdb=" N LYS G 55 " --> pdb=" O THR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 76 removed outlier: 3.780A pdb=" N LEU G 76 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 121 through 123 No H-bonds generated for 'chain 'G' and resid 121 through 123' Processing helix chain 'G' and resid 124 through 129 removed outlier: 3.920A pdb=" N LEU G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 153 Processing helix chain 'G' and resid 154 through 157 Processing helix chain 'G' and resid 158 through 177 Processing helix chain 'G' and resid 189 through 199 Processing helix chain 'G' and resid 261 through 265 removed outlier: 3.504A pdb=" N SER G 264 " --> pdb=" O HIS G 261 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN G 265 " --> pdb=" O ASP G 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 261 through 265' Processing helix chain 'G' and resid 287 through 309 removed outlier: 3.850A pdb=" N ASN G 309 " --> pdb=" O ILE G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 333 Processing helix chain 'G' and resid 358 through 362 removed outlier: 4.137A pdb=" N ASN G 361 " --> pdb=" O ASN G 358 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS G 362 " --> pdb=" O LYS G 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 358 through 362' Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 141 removed outlier: 5.713A pdb=" N ILE A 108 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG A 138 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE A 110 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE A 140 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN A 112 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR A 109 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR A 185 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU A 111 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE A 187 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE A 113 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY A 186 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG A 211 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 233 removed outlier: 3.938A pdb=" N THR A 232 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 276 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA A 248 " --> pdb=" O HIS A 316 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 318 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU A 250 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA A 320 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A 252 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 344 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE A 319 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 346 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TRP A 353 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 135 through 141 removed outlier: 6.438A pdb=" N ILE B 108 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG B 138 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE B 110 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE B 140 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN B 112 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B 182 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR B 209 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR B 184 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ARG B 211 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N GLY B 186 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 276 removed outlier: 3.620A pdb=" N TYR B 344 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE B 319 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE B 346 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP B 353 " --> pdb=" O HIS B 345 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 347 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 364 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 135 through 141 removed outlier: 6.147A pdb=" N ILE D 108 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG D 138 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE D 110 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE D 140 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN D 112 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG D 182 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYR D 209 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR D 184 " --> pdb=" O TYR D 209 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ARG D 211 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 232 through 233 removed outlier: 8.079A pdb=" N VAL D 273 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE D 249 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU D 275 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS D 251 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR D 344 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ILE D 319 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE D 346 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP D 353 " --> pdb=" O HIS D 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 135 through 141 removed outlier: 5.813A pdb=" N ILE E 108 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG E 138 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE E 110 " --> pdb=" O ARG E 138 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE E 140 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASN E 112 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR E 109 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR E 185 " --> pdb=" O TYR E 109 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU E 111 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE E 187 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE E 113 " --> pdb=" O ILE E 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 209 through 212 Processing sheet with id=AA9, first strand: chain 'E' and resid 232 through 233 removed outlier: 3.809A pdb=" N THR E 232 " --> pdb=" O LYS E 276 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS E 276 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR E 344 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE E 319 " --> pdb=" O TYR E 344 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE E 346 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP E 353 " --> pdb=" O HIS E 345 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR E 364 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 135 through 138 removed outlier: 6.105A pdb=" N ILE F 108 " --> pdb=" O LYS F 136 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG F 138 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE F 110 " --> pdb=" O ARG F 138 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG F 182 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TYR F 209 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR F 184 " --> pdb=" O TYR F 209 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG F 211 " --> pdb=" O TYR F 184 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N GLY F 186 " --> pdb=" O ARG F 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 272 through 276 removed outlier: 8.628A pdb=" N VAL F 273 " --> pdb=" O GLU F 247 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE F 249 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU F 275 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS F 251 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA F 248 " --> pdb=" O HIS F 316 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU F 318 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU F 250 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ALA F 320 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL F 252 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR F 344 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE F 319 " --> pdb=" O TYR F 344 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE F 346 " --> pdb=" O ILE F 319 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP F 353 " --> pdb=" O HIS F 345 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 364 " --> pdb=" O ILE F 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 135 through 141 removed outlier: 5.818A pdb=" N ILE G 108 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG G 138 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE G 110 " --> pdb=" O ARG G 138 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE G 140 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN G 112 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR G 109 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N THR G 185 " --> pdb=" O TYR G 109 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU G 111 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE G 187 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE G 113 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG G 182 " --> pdb=" O HIS G 207 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N TYR G 209 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR G 184 " --> pdb=" O TYR G 209 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ARG G 211 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N GLY G 186 " --> pdb=" O ARG G 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 232 through 233 removed outlier: 4.033A pdb=" N THR G 232 " --> pdb=" O LYS G 276 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS G 276 " --> pdb=" O THR G 232 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N VAL G 273 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE G 249 " --> pdb=" O VAL G 273 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU G 275 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS G 251 " --> pdb=" O LEU G 275 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA G 248 " --> pdb=" O HIS G 316 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU G 318 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU G 250 " --> pdb=" O LEU G 318 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR G 344 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE G 319 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE G 346 " --> pdb=" O ILE G 319 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP G 353 " --> pdb=" O HIS G 345 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR G 364 " --> pdb=" O ILE G 356 " (cutoff:3.500A) 757 hydrogen bonds defined for protein. 2175 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2715 1.31 - 1.43: 4390 1.43 - 1.56: 9837 1.56 - 1.68: 24 1.68 - 1.81: 18 Bond restraints: 16984 Sorted by residual: bond pdb=" C36 1SY B 401 " pdb=" N42 1SY B 401 " ideal model delta sigma weight residual 1.357 1.495 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C36 1SY G 401 " pdb=" N42 1SY G 401 " ideal model delta sigma weight residual 1.357 1.494 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C36 1SY E 401 " pdb=" N42 1SY E 401 " ideal model delta sigma weight residual 1.357 1.494 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C36 1SY D 401 " pdb=" N42 1SY D 401 " ideal model delta sigma weight residual 1.357 1.494 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C36 1SY A 401 " pdb=" N42 1SY A 401 " ideal model delta sigma weight residual 1.357 1.493 -0.136 2.00e-02 2.50e+03 4.65e+01 ... (remaining 16979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 22816 3.75 - 7.50: 140 7.50 - 11.26: 42 11.26 - 15.01: 30 15.01 - 18.76: 12 Bond angle restraints: 23040 Sorted by residual: angle pdb=" O19 1SY A 401 " pdb=" P18 1SY A 401 " pdb=" O44 1SY A 401 " ideal model delta sigma weight residual 123.21 104.45 18.76 3.00e+00 1.11e-01 3.91e+01 angle pdb=" O19 1SY F 401 " pdb=" P18 1SY F 401 " pdb=" O44 1SY F 401 " ideal model delta sigma weight residual 123.21 104.57 18.64 3.00e+00 1.11e-01 3.86e+01 angle pdb=" O19 1SY G 401 " pdb=" P18 1SY G 401 " pdb=" O44 1SY G 401 " ideal model delta sigma weight residual 123.21 104.57 18.64 3.00e+00 1.11e-01 3.86e+01 angle pdb=" O19 1SY D 401 " pdb=" P18 1SY D 401 " pdb=" O44 1SY D 401 " ideal model delta sigma weight residual 123.21 104.62 18.59 3.00e+00 1.11e-01 3.84e+01 angle pdb=" O19 1SY E 401 " pdb=" P18 1SY E 401 " pdb=" O44 1SY E 401 " ideal model delta sigma weight residual 123.21 104.65 18.56 3.00e+00 1.11e-01 3.83e+01 ... (remaining 23035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 9775 33.98 - 67.96: 506 67.96 - 101.93: 52 101.93 - 135.91: 18 135.91 - 169.89: 16 Dihedral angle restraints: 10367 sinusoidal: 4430 harmonic: 5937 Sorted by residual: dihedral pdb=" CA GLY A 287 " pdb=" C GLY A 287 " pdb=" N LYS A 288 " pdb=" CA LYS A 288 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" C25 1SY D 401 " pdb=" O26 1SY D 401 " pdb=" P27 1SY D 401 " pdb=" O30 1SY D 401 " ideal model delta sinusoidal sigma weight residual 344.98 175.09 169.89 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C25 1SY G 401 " pdb=" O26 1SY G 401 " pdb=" P27 1SY G 401 " pdb=" O30 1SY G 401 " ideal model delta sinusoidal sigma weight residual 344.98 175.83 169.15 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 10364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1918 0.041 - 0.082: 505 0.082 - 0.123: 187 0.123 - 0.164: 19 0.164 - 0.206: 12 Chirality restraints: 2641 Sorted by residual: chirality pdb=" C22 1SY F 401 " pdb=" C21 1SY F 401 " pdb=" C24 1SY F 401 " pdb=" O23 1SY F 401 " both_signs ideal model delta sigma weight residual False -2.70 -2.49 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL D 82 " pdb=" N VAL D 82 " pdb=" C VAL D 82 " pdb=" CB VAL D 82 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" C22 1SY E 401 " pdb=" C21 1SY E 401 " pdb=" C24 1SY E 401 " pdb=" O23 1SY E 401 " both_signs ideal model delta sigma weight residual False -2.70 -2.51 -0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 2638 not shown) Planarity restraints: 2876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 270 " -0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO D 271 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO D 271 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 271 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 288 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C LYS A 288 " 0.034 2.00e-02 2.50e+03 pdb=" O LYS A 288 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 289 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 40 " 0.012 2.00e-02 2.50e+03 1.35e-02 3.18e+00 pdb=" CG PHE B 40 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 40 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 40 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 40 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 40 " 0.002 2.00e-02 2.50e+03 ... (remaining 2873 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 613 2.71 - 3.26: 16471 3.26 - 3.81: 27305 3.81 - 4.35: 34675 4.35 - 4.90: 59321 Nonbonded interactions: 138385 Sorted by model distance: nonbonded pdb=" O ILE G 63 " pdb=" OG1 THR G 67 " model vdw 2.163 3.040 nonbonded pdb=" O VAL F 143 " pdb=" OG1 THR F 147 " model vdw 2.196 3.040 nonbonded pdb=" O GLU B 229 " pdb=" OH TYR B 294 " model vdw 2.204 3.040 nonbonded pdb=" O VAL B 143 " pdb=" OG1 THR B 147 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 63 " pdb=" OG1 THR B 67 " model vdw 2.235 3.040 ... (remaining 138380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 33 through 401) selection = (chain 'D' and resid 33 through 401) selection = (chain 'E' and resid 33 through 401) selection = (chain 'F' and resid 33 through 401) selection = (chain 'G' and resid 33 through 401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.730 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.138 16984 Z= 0.384 Angle : 0.968 18.760 23040 Z= 0.383 Chirality : 0.044 0.206 2641 Planarity : 0.004 0.085 2876 Dihedral : 21.403 169.888 6533 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.22 % Allowed : 27.46 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.20), residues: 2019 helix: 2.27 (0.19), residues: 812 sheet: -0.48 (0.28), residues: 365 loop : -0.41 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 120 TYR 0.015 0.001 TYR G 299 PHE 0.031 0.001 PHE B 40 TRP 0.007 0.001 TRP E 99 HIS 0.004 0.001 HIS F 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.38 (16984) covalent geometry : angle 0.96777 / 0.38 (23040) hydrogen bonds : bond 0.12627 / 8.57 ( 757) hydrogen bonds : angle 5.38266 / 3.84 ( 2175) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 233 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: D 38 ILE cc_start: 0.8100 (pt) cc_final: 0.7359 (mt) REVERT: F 294 TYR cc_start: 0.8907 (m-80) cc_final: 0.8435 (m-80) REVERT: F 335 ASP cc_start: 0.8325 (p0) cc_final: 0.7964 (p0) REVERT: G 118 ASP cc_start: 0.8263 (t0) cc_final: 0.8011 (t70) outliers start: 4 outliers final: 2 residues processed: 235 average time/residue: 0.1541 time to fit residues: 51.6621 Evaluate side-chains 223 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain G residue 215 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN E 322 GLN E 348 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.154736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118869 restraints weight = 21894.118| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.06 r_work: 0.3287 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16984 Z= 0.137 Angle : 0.511 7.673 23040 Z= 0.269 Chirality : 0.044 0.185 2641 Planarity : 0.004 0.059 2876 Dihedral : 20.362 179.659 2553 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.14 % Allowed : 25.04 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.20), residues: 2019 helix: 2.34 (0.18), residues: 843 sheet: -0.44 (0.29), residues: 376 loop : -0.27 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 120 TYR 0.018 0.001 TYR F 294 PHE 0.013 0.001 PHE A 146 TRP 0.010 0.001 TRP D 99 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16984) covalent geometry : angle 0.51066 / 0.27 (23040) hydrogen bonds : bond 0.04011 / 2.70 ( 757) hydrogen bonds : angle 4.33041 / 3.04 ( 2175) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.652 Fit side-chains REVERT: A 56 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7141 (mm) REVERT: A 106 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7872 (p0) REVERT: A 116 TYR cc_start: 0.8870 (m-10) cc_final: 0.8115 (m-80) REVERT: B 162 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8459 (mt) REVERT: B 165 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: B 230 GLU cc_start: 0.8505 (pm20) cc_final: 0.7898 (tt0) REVERT: D 38 ILE cc_start: 0.7831 (pt) cc_final: 0.7164 (mt) REVERT: D 103 LYS cc_start: 0.8035 (ptpt) cc_final: 0.7773 (pttt) REVERT: E 182 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8254 (mtt180) REVERT: E 303 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7812 (mtt-85) REVERT: F 169 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8657 (mttt) REVERT: F 294 TYR cc_start: 0.8900 (m-10) cc_final: 0.8515 (m-80) REVERT: G 275 LEU cc_start: 0.8583 (mt) cc_final: 0.8364 (mp) REVERT: G 332 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7934 (mp) outliers start: 39 outliers final: 19 residues processed: 271 average time/residue: 0.1551 time to fit residues: 60.4019 Evaluate side-chains 262 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 182 ARG Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 196 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 82 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121312 restraints weight = 22050.374| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.01 r_work: 0.3311 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16984 Z= 0.101 Angle : 0.480 7.680 23040 Z= 0.251 Chirality : 0.043 0.177 2641 Planarity : 0.004 0.047 2876 Dihedral : 19.299 179.874 2547 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.75 % Allowed : 24.11 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.20), residues: 2019 helix: 2.39 (0.18), residues: 852 sheet: -0.40 (0.29), residues: 378 loop : -0.21 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 314 TYR 0.014 0.001 TYR G 299 PHE 0.026 0.001 PHE B 40 TRP 0.010 0.001 TRP D 99 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (16984) covalent geometry : angle 0.48023 / 0.25 (23040) hydrogen bonds : bond 0.03529 / 2.39 ( 757) hydrogen bonds : angle 4.05287 / 2.83 ( 2175) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7223 (mm) REVERT: A 116 TYR cc_start: 0.8861 (m-10) cc_final: 0.7959 (m-10) REVERT: A 124 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8548 (m110) REVERT: B 162 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8520 (mt) REVERT: B 165 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: B 230 GLU cc_start: 0.8466 (pm20) cc_final: 0.7890 (tt0) REVERT: D 38 ILE cc_start: 0.7678 (pt) cc_final: 0.7040 (mt) REVERT: D 103 LYS cc_start: 0.7957 (ptpt) cc_final: 0.7596 (pttt) REVERT: F 161 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8050 (pt0) REVERT: F 169 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8618 (mttt) REVERT: F 228 PHE cc_start: 0.9001 (p90) cc_final: 0.8768 (p90) REVERT: F 294 TYR cc_start: 0.8870 (m-10) cc_final: 0.8577 (m-80) REVERT: G 275 LEU cc_start: 0.8673 (mt) cc_final: 0.8468 (mp) REVERT: G 332 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7730 (mp) outliers start: 50 outliers final: 21 residues processed: 279 average time/residue: 0.1525 time to fit residues: 61.3153 Evaluate side-chains 258 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 215 LYS Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 26 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 185 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 HIS ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 HIS G 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.155366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.119703 restraints weight = 21952.035| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.16 r_work: 0.3292 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16984 Z= 0.130 Angle : 0.499 7.850 23040 Z= 0.260 Chirality : 0.044 0.169 2641 Planarity : 0.004 0.042 2876 Dihedral : 18.739 178.800 2547 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.75 % Allowed : 23.78 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.20), residues: 2019 helix: 2.39 (0.18), residues: 853 sheet: -0.38 (0.28), residues: 375 loop : -0.24 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.013 0.001 TYR G 299 PHE 0.023 0.001 PHE B 40 TRP 0.011 0.001 TRP D 99 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (16984) covalent geometry : angle 0.49942 / 0.26 (23040) hydrogen bonds : bond 0.03648 / 2.46 ( 757) hydrogen bonds : angle 4.02667 / 2.82 ( 2175) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 0.762 Fit side-chains REVERT: A 56 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7202 (mm) REVERT: A 116 TYR cc_start: 0.8931 (m-10) cc_final: 0.8194 (m-80) REVERT: A 124 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8569 (m110) REVERT: A 346 PHE cc_start: 0.8538 (t80) cc_final: 0.8273 (t80) REVERT: B 162 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8524 (mt) REVERT: B 165 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: B 230 GLU cc_start: 0.8529 (pm20) cc_final: 0.7926 (tt0) REVERT: D 38 ILE cc_start: 0.7924 (pt) cc_final: 0.7217 (mt) REVERT: D 103 LYS cc_start: 0.7970 (ptpt) cc_final: 0.7619 (pttt) REVERT: D 144 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8673 (mtpp) REVERT: E 40 PHE cc_start: 0.8567 (t80) cc_final: 0.8122 (t80) REVERT: E 144 LYS cc_start: 0.8176 (tppt) cc_final: 0.7934 (tmtt) REVERT: E 182 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8291 (mtt180) REVERT: F 161 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: F 169 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8665 (mttt) REVERT: F 228 PHE cc_start: 0.9014 (p90) cc_final: 0.8792 (p90) REVERT: F 294 TYR cc_start: 0.8859 (m-10) cc_final: 0.8615 (m-80) REVERT: F 340 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7558 (tp30) REVERT: G 118 ASP cc_start: 0.8441 (t0) cc_final: 0.8185 (t0) REVERT: G 275 LEU cc_start: 0.8739 (mt) cc_final: 0.8531 (mp) REVERT: G 293 GLU cc_start: 0.8375 (tp30) cc_final: 0.8003 (tp30) outliers start: 50 outliers final: 29 residues processed: 276 average time/residue: 0.1593 time to fit residues: 63.5047 Evaluate side-chains 278 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 182 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 340 GLU Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN F 261 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.149337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113513 restraints weight = 21944.882| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.05 r_work: 0.3167 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 16984 Z= 0.279 Angle : 0.612 8.236 23040 Z= 0.316 Chirality : 0.047 0.190 2641 Planarity : 0.004 0.059 2876 Dihedral : 19.163 176.055 2547 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.68 % Allowed : 23.94 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2019 helix: 2.04 (0.18), residues: 849 sheet: -0.71 (0.28), residues: 367 loop : -0.28 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 120 TYR 0.018 0.002 TYR B 299 PHE 0.026 0.002 PHE F 365 TRP 0.012 0.001 TRP D 99 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.28 (16984) covalent geometry : angle 0.61216 / 0.32 (23040) hydrogen bonds : bond 0.04599 / 3.07 ( 757) hydrogen bonds : angle 4.35814 / 3.06 ( 2175) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 233 time to evaluate : 0.654 Fit side-chains REVERT: A 56 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7241 (mm) REVERT: B 116 TYR cc_start: 0.8984 (m-10) cc_final: 0.8716 (m-80) REVERT: B 162 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8674 (mt) REVERT: B 165 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: D 38 ILE cc_start: 0.8204 (pt) cc_final: 0.7648 (mt) REVERT: D 101 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8515 (mm) REVERT: D 103 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7835 (pttt) REVERT: E 182 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8538 (mtt180) REVERT: F 132 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: F 169 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8723 (mttt) REVERT: F 182 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7320 (mtm110) REVERT: F 294 TYR cc_start: 0.8948 (m-10) cc_final: 0.8607 (m-80) REVERT: G 293 GLU cc_start: 0.8324 (tp30) cc_final: 0.7983 (tp30) REVERT: G 332 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8087 (mp) outliers start: 67 outliers final: 45 residues processed: 284 average time/residue: 0.1615 time to fit residues: 65.6665 Evaluate side-chains 274 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 182 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 189 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN D 306 ASN D 358 ASN E 348 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119638 restraints weight = 21590.249| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.13 r_work: 0.3246 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16984 Z= 0.112 Angle : 0.503 8.008 23040 Z= 0.261 Chirality : 0.043 0.170 2641 Planarity : 0.004 0.045 2876 Dihedral : 18.594 179.224 2547 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.02 % Allowed : 24.99 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.20), residues: 2019 helix: 2.40 (0.18), residues: 845 sheet: -0.57 (0.28), residues: 370 loop : -0.28 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 120 TYR 0.014 0.001 TYR G 299 PHE 0.014 0.001 PHE A 146 TRP 0.013 0.001 TRP E 99 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (16984) covalent geometry : angle 0.50253 / 0.26 (23040) hydrogen bonds : bond 0.03592 / 2.42 ( 757) hydrogen bonds : angle 4.02772 / 2.82 ( 2175) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.598 Fit side-chains REVERT: A 56 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7137 (mm) REVERT: A 138 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7955 (mmp80) REVERT: B 165 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: B 171 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7647 (mp0) REVERT: D 38 ILE cc_start: 0.8160 (pt) cc_final: 0.7491 (mt) REVERT: D 103 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7784 (pttt) REVERT: E 107 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8311 (mtt-85) REVERT: F 132 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: F 169 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8638 (mttt) REVERT: F 294 TYR cc_start: 0.8922 (m-10) cc_final: 0.8680 (m-80) REVERT: G 118 ASP cc_start: 0.8112 (t0) cc_final: 0.7884 (t0) REVERT: G 293 GLU cc_start: 0.8258 (tp30) cc_final: 0.7905 (tp30) outliers start: 55 outliers final: 34 residues processed: 281 average time/residue: 0.1550 time to fit residues: 62.9953 Evaluate side-chains 271 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 215 LYS Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 141 optimal weight: 0.0770 chunk 163 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN E 348 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122029 restraints weight = 21634.686| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.02 r_work: 0.3266 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16984 Z= 0.118 Angle : 0.505 8.339 23040 Z= 0.262 Chirality : 0.043 0.171 2641 Planarity : 0.004 0.045 2876 Dihedral : 18.282 179.941 2547 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.64 % Allowed : 25.48 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.20), residues: 2019 helix: 2.41 (0.18), residues: 845 sheet: -0.57 (0.28), residues: 368 loop : -0.27 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 120 TYR 0.014 0.001 TYR G 299 PHE 0.029 0.001 PHE B 40 TRP 0.015 0.001 TRP D 99 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (16984) covalent geometry : angle 0.50541 / 0.26 (23040) hydrogen bonds : bond 0.03542 / 2.39 ( 757) hydrogen bonds : angle 3.99842 / 2.79 ( 2175) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: B 165 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: B 184 TYR cc_start: 0.8965 (t80) cc_final: 0.8745 (t80) REVERT: D 38 ILE cc_start: 0.8218 (pt) cc_final: 0.7684 (mt) REVERT: D 144 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8629 (mtpp) REVERT: E 40 PHE cc_start: 0.8694 (t80) cc_final: 0.8334 (t80) REVERT: E 107 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8309 (mtt-85) REVERT: E 182 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8479 (mtt180) REVERT: F 132 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: F 169 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8591 (mttt) REVERT: G 118 ASP cc_start: 0.8343 (t0) cc_final: 0.8125 (t0) REVERT: G 350 ARG cc_start: 0.7432 (ptm160) cc_final: 0.7047 (ptm160) outliers start: 48 outliers final: 35 residues processed: 270 average time/residue: 0.1583 time to fit residues: 61.3719 Evaluate side-chains 264 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 107 ARG Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 182 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 215 LYS Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 10 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 167 optimal weight: 0.0010 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 348 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.154084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118839 restraints weight = 21612.856| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.00 r_work: 0.3272 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16984 Z= 0.113 Angle : 0.503 8.591 23040 Z= 0.261 Chirality : 0.043 0.175 2641 Planarity : 0.004 0.045 2876 Dihedral : 18.133 179.605 2547 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.80 % Allowed : 25.54 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.20), residues: 2019 helix: 2.44 (0.18), residues: 845 sheet: -0.55 (0.28), residues: 368 loop : -0.26 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 120 TYR 0.014 0.001 TYR F 102 PHE 0.025 0.001 PHE B 40 TRP 0.014 0.001 TRP D 99 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (16984) covalent geometry : angle 0.50271 / 0.26 (23040) hydrogen bonds : bond 0.03486 / 2.35 ( 757) hydrogen bonds : angle 3.97032 / 2.77 ( 2175) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 348 ASN cc_start: 0.7640 (t0) cc_final: 0.7435 (t0) REVERT: B 165 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: B 171 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7606 (mp0) REVERT: D 38 ILE cc_start: 0.8182 (pt) cc_final: 0.7670 (mt) REVERT: E 182 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8475 (mtt180) REVERT: E 278 ASP cc_start: 0.7853 (m-30) cc_final: 0.7528 (m-30) REVERT: F 132 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: F 169 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8577 (mttt) REVERT: F 294 TYR cc_start: 0.8920 (m-80) cc_final: 0.8468 (m-80) REVERT: G 350 ARG cc_start: 0.7406 (ptm160) cc_final: 0.7131 (ptm160) outliers start: 51 outliers final: 37 residues processed: 268 average time/residue: 0.1585 time to fit residues: 61.1958 Evaluate side-chains 263 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 182 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 141 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 186 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN B 360 HIS D 306 ASN E 348 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.153596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118135 restraints weight = 21922.805| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.04 r_work: 0.3214 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 16984 Z= 0.184 Angle : 0.551 8.988 23040 Z= 0.286 Chirality : 0.045 0.178 2641 Planarity : 0.004 0.046 2876 Dihedral : 18.487 179.865 2547 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.86 % Allowed : 25.54 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.20), residues: 2019 helix: 2.26 (0.18), residues: 847 sheet: -0.78 (0.28), residues: 365 loop : -0.28 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 120 TYR 0.015 0.001 TYR D 299 PHE 0.035 0.002 PHE A 346 TRP 0.012 0.001 TRP D 99 HIS 0.006 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (16984) covalent geometry : angle 0.55055 / 0.29 (23040) hydrogen bonds : bond 0.03950 / 2.64 ( 757) hydrogen bonds : angle 4.12454 / 2.88 ( 2175) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7148 (mm) REVERT: A 138 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7912 (mmp80) REVERT: B 161 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7323 (mt-10) REVERT: B 165 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: B 184 TYR cc_start: 0.9089 (t80) cc_final: 0.8854 (t80) REVERT: D 38 ILE cc_start: 0.8186 (pt) cc_final: 0.7660 (mt) REVERT: D 144 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8674 (mtpp) REVERT: E 40 PHE cc_start: 0.8754 (t80) cc_final: 0.8384 (t80) REVERT: E 182 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8528 (mtt180) REVERT: F 132 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: F 169 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8647 (mttt) REVERT: F 294 TYR cc_start: 0.8945 (m-80) cc_final: 0.8362 (m-80) REVERT: G 118 ASP cc_start: 0.8360 (t0) cc_final: 0.8108 (t70) REVERT: G 274 ASP cc_start: 0.7525 (t0) cc_final: 0.7304 (t0) REVERT: G 350 ARG cc_start: 0.7433 (ptm160) cc_final: 0.7211 (ptm160) outliers start: 52 outliers final: 39 residues processed: 273 average time/residue: 0.1534 time to fit residues: 60.0673 Evaluate side-chains 265 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 182 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 165 optimal weight: 0.0170 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 306 ASN E 348 ASN F 68 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.154710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120039 restraints weight = 21575.699| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.97 r_work: 0.3270 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16984 Z= 0.118 Angle : 0.514 8.949 23040 Z= 0.268 Chirality : 0.044 0.180 2641 Planarity : 0.004 0.045 2876 Dihedral : 18.236 179.769 2547 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.64 % Allowed : 25.76 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.20), residues: 2019 helix: 2.33 (0.18), residues: 848 sheet: -0.68 (0.28), residues: 363 loop : -0.27 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 120 TYR 0.014 0.001 TYR E 299 PHE 0.033 0.001 PHE A 346 TRP 0.014 0.001 TRP D 99 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (16984) covalent geometry : angle 0.51419 / 0.27 (23040) hydrogen bonds : bond 0.03511 / 2.36 ( 757) hydrogen bonds : angle 3.99830 / 2.79 ( 2175) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4038 Ramachandran restraints generated. 2019 Oldfield, 0 Emsley, 2019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 138 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7908 (mmp80) REVERT: B 161 GLU cc_start: 0.7815 (mt-10) cc_final: 0.6992 (mt-10) REVERT: B 165 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: B 171 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7668 (mp0) REVERT: D 38 ILE cc_start: 0.8172 (pt) cc_final: 0.7629 (mt) REVERT: D 144 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8615 (mtpp) REVERT: E 40 PHE cc_start: 0.8644 (t80) cc_final: 0.8281 (t80) REVERT: E 182 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8475 (mtt180) REVERT: E 278 ASP cc_start: 0.7908 (m-30) cc_final: 0.7662 (m-30) REVERT: F 132 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: F 169 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8616 (mttt) REVERT: F 294 TYR cc_start: 0.8861 (m-80) cc_final: 0.8398 (m-80) REVERT: G 350 ARG cc_start: 0.7402 (ptm160) cc_final: 0.7142 (ptm160) outliers start: 48 outliers final: 37 residues processed: 262 average time/residue: 0.1583 time to fit residues: 59.5538 Evaluate side-chains 266 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 182 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 269 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 278 ASP Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 104 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 306 ASN E 348 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.151212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115665 restraints weight = 21791.573| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.99 r_work: 0.3210 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 16984 Z= 0.213 Angle : 0.573 9.073 23040 Z= 0.297 Chirality : 0.046 0.187 2641 Planarity : 0.004 0.045 2876 Dihedral : 18.578 178.823 2547 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.86 % Allowed : 25.54 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.19), residues: 2019 helix: 2.19 (0.18), residues: 846 sheet: -0.89 (0.27), residues: 365 loop : -0.31 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 120 TYR 0.015 0.002 TYR B 299 PHE 0.033 0.002 PHE A 346 TRP 0.011 0.001 TRP D 99 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.21 (16984) covalent geometry : angle 0.57263 / 0.30 (23040) hydrogen bonds : bond 0.04083 / 2.73 ( 757) hydrogen bonds : angle 4.17310 / 2.92 ( 2175) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4473.16 seconds wall clock time: 77 minutes 25.97 seconds (4645.97 seconds total)