Starting phenix.real_space_refine on Thu Aug 6 14:15:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8e_34544/08_2026/8h8e_34544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8e_34544/08_2026/8h8e_34544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h8e_34544/08_2026/8h8e_34544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8e_34544/08_2026/8h8e_34544.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h8e_34544/08_2026/8h8e_34544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8e_34544/08_2026/8h8e_34544.map" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 74 5.49 5 S 78 5.16 5 C 9962 2.51 5 N 2662 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15818 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2366 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 275} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2337 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain: "C" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2351 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2425 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain: "E" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2392 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 12, 'TRANS': 276} Chain: "F" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2354 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "G" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1593 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 28, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 58} Time building chain proxies: 4.07, per 1000 atoms: 0.26 Number of scatterers: 15818 At special positions: 0 Unit cell: (96.28, 151.06, 141.93, 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 78 16.00 P 74 15.00 O 3042 8.00 N 2662 7.00 C 9962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 151 " distance=2.03 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 151 " distance=2.03 Simple disulfide: pdb=" SG CYS F 129 " - pdb=" SG CYS F 151 " distance=2.03 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: 1.50 Conformation dependent library (CDL) restraints added in 668.9 milliseconds 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3326 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 29 sheets defined 34.9% alpha, 23.9% beta 22 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 56 through 99 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.986A pdb=" N CYS A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 343 Processing helix chain 'B' and resid 61 through 99 removed outlier: 3.778A pdb=" N LEU B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 334 Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.804A pdb=" N HIS B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 69 through 99 removed outlier: 3.597A pdb=" N TYR C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.651A pdb=" N LYS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 226 removed outlier: 3.738A pdb=" N MET C 222 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 226 " --> pdb=" O MET C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 345 Processing helix chain 'D' and resid 59 through 99 removed outlier: 3.854A pdb=" N ASN D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL D 83 " --> pdb=" O MET D 79 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.789A pdb=" N MET D 222 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 304 through 349 removed outlier: 3.797A pdb=" N MET D 308 " --> pdb=" O ASN D 304 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 99 removed outlier: 3.759A pdb=" N SER E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET E 79 " --> pdb=" O TYR E 75 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE E 84 " --> pdb=" O GLY E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.548A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 229 removed outlier: 3.556A pdb=" N MET E 222 " --> pdb=" O GLN E 218 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 226 " --> pdb=" O MET E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 4.415A pdb=" N LYS E 278 " --> pdb=" O THR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 342 removed outlier: 3.969A pdb=" N ALA E 310 " --> pdb=" O TRP E 306 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG E 337 " --> pdb=" O MET E 333 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG E 338 " --> pdb=" O ILE E 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS E 342 " --> pdb=" O ARG E 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 96 removed outlier: 3.880A pdb=" N LEU F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 71 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE F 72 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'F' and resid 217 through 229 removed outlier: 3.738A pdb=" N CYS F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 227 " --> pdb=" O GLN F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 342 removed outlier: 3.649A pdb=" N MET F 308 " --> pdb=" O ASN F 304 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU F 317 " --> pdb=" O CYS F 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 331 " --> pdb=" O LYS F 327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108 removed outlier: 3.621A pdb=" N ILE A 294 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 285 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 287 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 186 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N HIS A 190 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 126 " --> pdb=" O HIS A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 108 removed outlier: 3.621A pdb=" N ILE A 294 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE A 238 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL A 286 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 240 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLU A 288 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL A 242 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS A 290 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N MET A 244 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N LEU A 246 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A 294 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LYS A 248 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 296 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS A 250 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLN A 298 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 243 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 263 " --> pdb=" O LYS A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 158 removed outlier: 3.791A pdb=" N ILE A 172 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 156 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 119 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 173 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 201 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 234 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 232 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 104 removed outlier: 8.193A pdb=" N TYR B 293 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 246 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 295 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 299 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP B 241 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 243 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 108 removed outlier: 8.193A pdb=" N TYR B 293 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 246 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 295 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 299 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 286 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 119 removed outlier: 3.535A pdb=" N PHE B 234 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.589A pdb=" N ARG B 125 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 190 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 281 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 159 removed outlier: 3.631A pdb=" N ILE B 156 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 101 through 108 removed outlier: 6.471A pdb=" N LEU C 246 " --> pdb=" O GLN C 295 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE C 297 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LYS C 248 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP C 299 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS C 250 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 117 removed outlier: 3.636A pdb=" N PHE C 206 " --> pdb=" O GLY C 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 126 through 132 removed outlier: 6.213A pdb=" N GLN C 188 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS C 129 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE C 186 " --> pdb=" O CYS C 129 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N HIS C 131 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 184 " --> pdb=" O HIS C 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.844A pdb=" N ILE C 172 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 158 through 159 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB7, first strand: chain 'C' and resid 264 through 265 removed outlier: 3.718A pdb=" N TRP C 241 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR C 240 " --> pdb=" O VAL C 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 105 removed outlier: 9.924A pdb=" N GLN D 295 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 246 " --> pdb=" O GLN D 295 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE D 297 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS D 248 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR D 240 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU D 288 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL D 242 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN D 281 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 191 " --> pdb=" O GLN D 281 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 285 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN D 188 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS D 190 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 103 through 105 removed outlier: 9.924A pdb=" N GLN D 295 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 246 " --> pdb=" O GLN D 295 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE D 297 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS D 248 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 243 " --> pdb=" O GLU D 263 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 257 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 173 through 174 removed outlier: 3.505A pdb=" N PHE D 234 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP D 232 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 158 through 159 removed outlier: 3.946A pdb=" N TYR D 158 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 168 " --> pdb=" O TYR D 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 101 through 108 removed outlier: 3.944A pdb=" N SER E 105 " --> pdb=" O GLU E 296 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 296 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 14.566A pdb=" N TYR E 293 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N MET E 244 " --> pdb=" O TYR E 293 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N GLN E 295 " --> pdb=" O MET E 244 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU E 246 " --> pdb=" O GLN E 295 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE E 297 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS E 248 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASP E 299 " --> pdb=" O LYS E 248 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS E 243 " --> pdb=" O GLU E 263 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR E 249 " --> pdb=" O SER E 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 101 through 108 removed outlier: 3.944A pdb=" N SER E 105 " --> pdb=" O GLU E 296 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 296 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 14.566A pdb=" N TYR E 293 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N MET E 244 " --> pdb=" O TYR E 293 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N GLN E 295 " --> pdb=" O MET E 244 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU E 246 " --> pdb=" O GLN E 295 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE E 297 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS E 248 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASP E 299 " --> pdb=" O LYS E 248 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU E 288 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 118 through 120 removed outlier: 4.108A pdb=" N ASP E 202 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC7, first strand: chain 'F' and resid 100 through 107 removed outlier: 3.567A pdb=" N GLN F 295 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 259 " --> pdb=" O VAL F 247 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 100 through 107 removed outlier: 3.567A pdb=" N GLN F 295 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 117 through 120 removed outlier: 4.017A pdb=" N ASP F 202 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AD2, first strand: chain 'F' and resid 239 through 240 636 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4665 1.34 - 1.46: 3968 1.46 - 1.58: 7478 1.58 - 1.70: 148 1.70 - 1.82: 126 Bond restraints: 16385 Sorted by residual: bond pdb=" C ASP F 197 " pdb=" N PHE F 198 " ideal model delta sigma weight residual 1.331 1.292 0.039 1.34e-02 5.57e+03 8.29e+00 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.78e+00 bond pdb=" N LEU A 77 " pdb=" CA LEU A 77 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.21e+00 bond pdb=" N LEU A 73 " pdb=" CA LEU A 73 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.02e+00 bond pdb=" N LEU F 71 " pdb=" CA LEU F 71 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 5.13e+00 ... (remaining 16380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 21993 2.15 - 4.30: 469 4.30 - 6.45: 39 6.45 - 8.60: 13 8.60 - 10.75: 3 Bond angle restraints: 22517 Sorted by residual: angle pdb=" N TYR C 112 " pdb=" CA TYR C 112 " pdb=" C TYR C 112 " ideal model delta sigma weight residual 111.02 121.77 -10.75 1.22e+00 6.72e-01 7.76e+01 angle pdb=" N MET C 111 " pdb=" CA MET C 111 " pdb=" C MET C 111 " ideal model delta sigma weight residual 108.23 116.66 -8.43 1.38e+00 5.25e-01 3.73e+01 angle pdb=" N HIS A 132 " pdb=" CA HIS A 132 " pdb=" C HIS A 132 " ideal model delta sigma weight residual 109.15 100.39 8.76 1.44e+00 4.82e-01 3.70e+01 angle pdb=" N TRP A 133 " pdb=" CA TRP A 133 " pdb=" C TRP A 133 " ideal model delta sigma weight residual 110.17 101.71 8.46 1.61e+00 3.86e-01 2.76e+01 angle pdb=" O5' U G 16 " pdb=" C5' U G 16 " pdb=" C4' U G 16 " ideal model delta sigma weight residual 109.40 113.32 -3.92 8.00e-01 1.56e+00 2.40e+01 ... (remaining 22512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 9526 35.43 - 70.85: 354 70.85 - 106.28: 44 106.28 - 141.70: 2 141.70 - 177.13: 3 Dihedral angle restraints: 9929 sinusoidal: 4821 harmonic: 5108 Sorted by residual: dihedral pdb=" O4' C G 74 " pdb=" C1' C G 74 " pdb=" N1 C G 74 " pdb=" C2 C G 74 " ideal model delta sinusoidal sigma weight residual -128.00 49.13 -177.13 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CB CYS E 129 " pdb=" SG CYS E 129 " pdb=" SG CYS E 151 " pdb=" CB CYS E 151 " ideal model delta sinusoidal sigma weight residual 93.00 23.89 69.11 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CB CYS D 129 " pdb=" SG CYS D 129 " pdb=" SG CYS D 151 " pdb=" CB CYS D 151 " ideal model delta sinusoidal sigma weight residual 93.00 29.59 63.41 1 1.00e+01 1.00e-02 5.30e+01 ... (remaining 9926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1941 0.048 - 0.095: 410 0.095 - 0.143: 148 0.143 - 0.191: 14 0.191 - 0.239: 4 Chirality restraints: 2517 Sorted by residual: chirality pdb=" CB ILE A 201 " pdb=" CA ILE A 201 " pdb=" CG1 ILE A 201 " pdb=" CG2 ILE A 201 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP A 197 " pdb=" N ASP A 197 " pdb=" C ASP A 197 " pdb=" CB ASP A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA TYR C 112 " pdb=" N TYR C 112 " pdb=" C TYR C 112 " pdb=" CB TYR C 112 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2514 not shown) Planarity restraints: 2553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 158 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C TYR A 158 " 0.047 2.00e-02 2.50e+03 pdb=" O TYR A 158 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE A 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 133 " -0.015 2.00e-02 2.50e+03 1.47e-02 5.42e+00 pdb=" CG TRP C 133 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 133 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 133 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 133 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 133 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 133 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 133 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 133 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 133 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 142 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO D 143 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 143 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 143 " 0.030 5.00e-02 4.00e+02 ... (remaining 2550 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1932 2.75 - 3.29: 16526 3.29 - 3.82: 27055 3.82 - 4.36: 30269 4.36 - 4.90: 49794 Nonbonded interactions: 125576 Sorted by model distance: nonbonded pdb=" O4 U G 33 " pdb=" N4 C G 38 " model vdw 2.210 3.120 nonbonded pdb=" O ASP D 224 " pdb=" OG SER D 228 " model vdw 2.229 3.040 nonbonded pdb=" O2' G G 17 " pdb=" N2 G G 56 " model vdw 2.236 3.120 nonbonded pdb=" OE2 GLU B 263 " pdb=" NZ LYS B 290 " model vdw 2.239 3.120 nonbonded pdb=" OG1 THR D 194 " pdb=" OE1 GLN D 196 " model vdw 2.243 3.040 ... (remaining 125571 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' and resid 61 through 342) selection = (chain 'B' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) selection = (chain 'C' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) selection = (chain 'D' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) selection = (chain 'E' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) selection = (chain 'F' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) } 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 group one per residue 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 16.960 Find NCS groups from input model: 0.290 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 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 : 0.003 0.086 16391 Z= 0.172 Angle : 0.691 10.748 22529 Z= 0.425 Chirality : 0.047 0.239 2517 Planarity : 0.004 0.055 2553 Dihedral : 17.899 177.125 6585 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.43 % 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: -2.48 (0.21), residues: 1711 helix: 0.80 (0.22), residues: 556 sheet: -3.15 (0.21), residues: 520 loop : -2.37 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.026 0.001 TYR C 112 PHE 0.025 0.002 PHE C 198 TRP 0.039 0.002 TRP C 133 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (16385) covalent geometry : angle 0.69019 / 0.42 (22517) SS BOND : bond 0.00296 / 0.14 ( 6) SS BOND : angle 1.37639 / 0.79 ( 12) hydrogen bonds : bond 0.16239 / 11.54 ( 662) hydrogen bonds : angle 7.50673 / 5.06 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.6865 (ppp) cc_final: 0.6584 (ppp) REVERT: B 308 MET cc_start: 0.7037 (ppp) cc_final: 0.6703 (ppp) REVERT: E 244 MET cc_start: 0.8458 (ptp) cc_final: 0.8217 (ptt) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1091 time to fit residues: 39.2406 Evaluate side-chains 179 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 HIS C 174 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 HIS ** 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 = 0.4482 r_free = 0.4482 target = 0.150484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.105656 restraints weight = 38911.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.107750 restraints weight = 29102.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.109077 restraints weight = 23932.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.109746 restraints weight = 21175.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.110381 restraints weight = 19718.205| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16391 Z= 0.156 Angle : 0.628 13.665 22529 Z= 0.328 Chirality : 0.041 0.192 2517 Planarity : 0.005 0.072 2553 Dihedral : 17.639 178.907 3065 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.29 % Favored : 90.65 % Rotamer: Outliers : 1.58 % Allowed : 9.53 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.31 (0.21), residues: 1711 helix: 0.96 (0.22), residues: 551 sheet: -3.02 (0.20), residues: 534 loop : -2.27 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 177 TYR 0.029 0.002 TYR C 162 PHE 0.037 0.002 PHE C 234 TRP 0.030 0.002 TRP C 133 HIS 0.004 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (16385) covalent geometry : angle 0.62699 / 0.33 (22517) SS BOND : bond 0.00274 / 0.17 ( 6) SS BOND : angle 1.79577 / 0.94 ( 12) hydrogen bonds : bond 0.04445 / 2.95 ( 662) hydrogen bonds : angle 5.51867 / 3.78 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7253 (t80) REVERT: A 330 VAL cc_start: 0.7834 (t) cc_final: 0.7609 (t) REVERT: B 308 MET cc_start: 0.8899 (ppp) cc_final: 0.8293 (ppp) REVERT: E 66 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7796 (t80) REVERT: E 244 MET cc_start: 0.8735 (ptp) cc_final: 0.8532 (ptt) REVERT: F 95 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.8023 (t0) outliers start: 25 outliers final: 16 residues processed: 211 average time/residue: 0.1080 time to fit residues: 36.1807 Evaluate side-chains 195 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 174 optimal weight: 50.0000 chunk 29 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 172 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 146 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.149654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.107016 restraints weight = 39400.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.108023 restraints weight = 30608.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.107676 restraints weight = 24526.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.107934 restraints weight = 25550.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.108027 restraints weight = 23967.049| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16391 Z= 0.169 Angle : 0.597 14.351 22529 Z= 0.314 Chirality : 0.040 0.214 2517 Planarity : 0.004 0.047 2553 Dihedral : 17.558 179.170 3065 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 1.89 % Allowed : 12.81 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.26 (0.21), residues: 1711 helix: 0.96 (0.22), residues: 552 sheet: -2.95 (0.21), residues: 523 loop : -2.28 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 182 TYR 0.024 0.002 TYR C 75 PHE 0.026 0.002 PHE C 234 TRP 0.030 0.002 TRP C 133 HIS 0.004 0.001 HIS F 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (16385) covalent geometry : angle 0.59533 / 0.31 (22517) SS BOND : bond 0.00301 / 0.16 ( 6) SS BOND : angle 1.82303 / 0.96 ( 12) hydrogen bonds : bond 0.04188 / 2.84 ( 662) hydrogen bonds : angle 5.13672 / 3.54 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7137 (t80) REVERT: B 308 MET cc_start: 0.8819 (ppp) cc_final: 0.8324 (ppp) REVERT: D 152 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7750 (t) REVERT: E 66 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7579 (t80) REVERT: E 263 GLU cc_start: 0.8212 (mp0) cc_final: 0.8001 (mt-10) REVERT: E 333 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7455 (ptm) REVERT: F 158 TYR cc_start: 0.5436 (m-80) cc_final: 0.5054 (m-80) outliers start: 30 outliers final: 19 residues processed: 204 average time/residue: 0.0953 time to fit residues: 30.9041 Evaluate side-chains 193 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.150846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.107920 restraints weight = 39092.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.109183 restraints weight = 29583.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.110236 restraints weight = 24847.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.109964 restraints weight = 23331.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.110093 restraints weight = 22121.932| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16391 Z= 0.132 Angle : 0.585 14.582 22529 Z= 0.300 Chirality : 0.040 0.265 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.492 178.824 3065 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 1.89 % Allowed : 14.64 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.16 (0.21), residues: 1711 helix: 1.00 (0.21), residues: 563 sheet: -2.91 (0.21), residues: 531 loop : -2.21 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 177 TYR 0.023 0.001 TYR C 75 PHE 0.023 0.001 PHE C 234 TRP 0.024 0.002 TRP D 306 HIS 0.003 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16385) covalent geometry : angle 0.58323 / 0.30 (22517) SS BOND : bond 0.00576 / 0.30 ( 6) SS BOND : angle 1.85233 / 1.01 ( 12) hydrogen bonds : bond 0.03811 / 2.62 ( 662) hydrogen bonds : angle 4.88972 / 3.37 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7163 (t80) REVERT: B 308 MET cc_start: 0.8629 (ppp) cc_final: 0.8249 (ppp) REVERT: E 66 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7523 (t80) REVERT: F 95 ASP cc_start: 0.8205 (t0) cc_final: 0.7759 (t0) REVERT: F 181 ARG cc_start: 0.6728 (tpm170) cc_final: 0.6443 (tpm170) outliers start: 30 outliers final: 21 residues processed: 205 average time/residue: 0.0919 time to fit residues: 30.2944 Evaluate side-chains 198 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 129 optimal weight: 0.3980 chunk 173 optimal weight: 50.0000 chunk 112 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 108 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.140108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.097053 restraints weight = 36052.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.098392 restraints weight = 28574.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.098227 restraints weight = 23993.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.098443 restraints weight = 25154.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.098599 restraints weight = 23931.727| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16391 Z= 0.118 Angle : 0.594 15.037 22529 Z= 0.301 Chirality : 0.040 0.222 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.426 178.497 3065 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.70 % Allowed : 16.28 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.07 (0.21), residues: 1711 helix: 1.01 (0.21), residues: 562 sheet: -2.79 (0.21), residues: 528 loop : -2.16 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.017 0.001 TYR C 162 PHE 0.021 0.001 PHE C 234 TRP 0.037 0.002 TRP C 133 HIS 0.006 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (16385) covalent geometry : angle 0.59320 / 0.30 (22517) SS BOND : bond 0.00234 / 0.14 ( 6) SS BOND : angle 1.64863 / 0.89 ( 12) hydrogen bonds : bond 0.03708 / 2.54 ( 662) hydrogen bonds : angle 4.73358 / 3.26 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7178 (t80) REVERT: A 330 VAL cc_start: 0.8044 (t) cc_final: 0.7829 (t) REVERT: B 308 MET cc_start: 0.8679 (ppp) cc_final: 0.8261 (ppp) REVERT: D 297 ILE cc_start: 0.8689 (mm) cc_final: 0.8383 (tt) REVERT: F 95 ASP cc_start: 0.8252 (t0) cc_final: 0.7791 (t0) REVERT: F 181 ARG cc_start: 0.6907 (tpm170) cc_final: 0.6586 (tpm170) outliers start: 27 outliers final: 23 residues processed: 211 average time/residue: 0.0986 time to fit residues: 33.0899 Evaluate side-chains 199 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 171 optimal weight: 50.0000 chunk 91 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN D 169 HIS D 188 GLN F 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.137694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093427 restraints weight = 35793.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.094926 restraints weight = 30037.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094524 restraints weight = 25841.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094821 restraints weight = 26158.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.094904 restraints weight = 24684.417| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16391 Z= 0.171 Angle : 0.601 14.481 22529 Z= 0.310 Chirality : 0.040 0.220 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.437 179.163 3065 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 2.90 % Allowed : 16.97 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.13 (0.21), residues: 1711 helix: 1.03 (0.21), residues: 559 sheet: -2.84 (0.21), residues: 538 loop : -2.20 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 177 TYR 0.025 0.002 TYR F 158 PHE 0.043 0.002 PHE C 234 TRP 0.028 0.002 TRP F 289 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (16385) covalent geometry : angle 0.59953 / 0.31 (22517) SS BOND : bond 0.00358 / 0.19 ( 6) SS BOND : angle 1.83139 / 0.98 ( 12) hydrogen bonds : bond 0.03795 / 2.62 ( 662) hydrogen bonds : angle 4.68798 / 3.23 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7202 (t80) REVERT: A 330 VAL cc_start: 0.8092 (t) cc_final: 0.7859 (t) REVERT: C 167 MET cc_start: 0.7535 (tpt) cc_final: 0.7227 (tpt) REVERT: D 297 ILE cc_start: 0.8733 (mm) cc_final: 0.8416 (tt) REVERT: E 66 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7735 (t80) REVERT: F 95 ASP cc_start: 0.8395 (t0) cc_final: 0.7868 (t0) REVERT: F 177 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7402 (mtp-110) REVERT: F 181 ARG cc_start: 0.7015 (tpm170) cc_final: 0.6590 (tpm170) outliers start: 46 outliers final: 29 residues processed: 210 average time/residue: 0.0991 time to fit residues: 32.9420 Evaluate side-chains 202 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 93 optimal weight: 0.0270 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.140196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.097741 restraints weight = 35960.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.098854 restraints weight = 29883.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.098804 restraints weight = 25306.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.098921 restraints weight = 25936.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.099081 restraints weight = 24400.825| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16391 Z= 0.113 Angle : 0.593 14.465 22529 Z= 0.297 Chirality : 0.040 0.226 2517 Planarity : 0.004 0.045 2553 Dihedral : 17.395 178.585 3065 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.15 % Allowed : 18.49 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.05 (0.21), residues: 1711 helix: 1.03 (0.21), residues: 566 sheet: -2.74 (0.21), residues: 539 loop : -2.18 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.018 0.001 TYR A 134 PHE 0.031 0.001 PHE C 234 TRP 0.042 0.002 TRP F 289 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (16385) covalent geometry : angle 0.59229 / 0.30 (22517) SS BOND : bond 0.00168 / 0.11 ( 6) SS BOND : angle 1.50397 / 0.79 ( 12) hydrogen bonds : bond 0.03544 / 2.44 ( 662) hydrogen bonds : angle 4.55226 / 3.14 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7162 (t80) REVERT: A 330 VAL cc_start: 0.8068 (t) cc_final: 0.7820 (t) REVERT: B 308 MET cc_start: 0.8766 (ppp) cc_final: 0.8145 (ppp) REVERT: C 167 MET cc_start: 0.7399 (tpt) cc_final: 0.7116 (tpt) REVERT: D 297 ILE cc_start: 0.8700 (mm) cc_final: 0.8392 (tt) REVERT: E 66 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7682 (t80) REVERT: F 95 ASP cc_start: 0.8313 (t0) cc_final: 0.7800 (t0) REVERT: F 181 ARG cc_start: 0.6894 (tpm170) cc_final: 0.6574 (tpm170) REVERT: F 222 MET cc_start: 0.7905 (tmm) cc_final: 0.7698 (tmm) outliers start: 34 outliers final: 25 residues processed: 205 average time/residue: 0.0932 time to fit residues: 30.4636 Evaluate side-chains 197 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 10 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.1345 > 50:) chunk 67 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.138094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.094335 restraints weight = 35991.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095495 restraints weight = 29800.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095174 restraints weight = 25082.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.095495 restraints weight = 25061.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095612 restraints weight = 24025.210| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16391 Z= 0.168 Angle : 0.627 14.505 22529 Z= 0.315 Chirality : 0.040 0.218 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.413 179.172 3065 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.33 % Allowed : 19.12 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.08 (0.21), residues: 1711 helix: 1.01 (0.21), residues: 559 sheet: -2.75 (0.21), residues: 534 loop : -2.18 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.030 0.002 TYR F 158 PHE 0.028 0.002 PHE C 234 TRP 0.048 0.002 TRP C 133 HIS 0.005 0.001 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (16385) covalent geometry : angle 0.62590 / 0.31 (22517) SS BOND : bond 0.00327 / 0.15 ( 6) SS BOND : angle 1.63082 / 0.87 ( 12) hydrogen bonds : bond 0.03698 / 2.55 ( 662) hydrogen bonds : angle 4.57461 / 3.14 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7209 (t80) REVERT: A 330 VAL cc_start: 0.8075 (t) cc_final: 0.7847 (t) REVERT: B 308 MET cc_start: 0.8817 (ppp) cc_final: 0.8248 (ppp) REVERT: C 167 MET cc_start: 0.7534 (tpt) cc_final: 0.7248 (tpt) REVERT: D 297 ILE cc_start: 0.8719 (mm) cc_final: 0.8388 (tt) REVERT: E 66 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7509 (t80) REVERT: F 95 ASP cc_start: 0.8390 (t0) cc_final: 0.7868 (t0) REVERT: F 177 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7499 (tpp-160) REVERT: F 181 ARG cc_start: 0.6898 (tpm170) cc_final: 0.6551 (tpm170) REVERT: F 222 MET cc_start: 0.7964 (tmm) cc_final: 0.7217 (tmm) outliers start: 37 outliers final: 30 residues processed: 200 average time/residue: 0.0948 time to fit residues: 30.1706 Evaluate side-chains 203 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.135705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094070 restraints weight = 35800.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093682 restraints weight = 30144.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.093646 restraints weight = 29936.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.093873 restraints weight = 30175.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.093967 restraints weight = 27584.197| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16391 Z= 0.242 Angle : 0.680 15.499 22529 Z= 0.347 Chirality : 0.043 0.230 2517 Planarity : 0.005 0.047 2553 Dihedral : 17.513 179.783 3065 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 2.15 % Allowed : 19.56 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.32 (0.21), residues: 1711 helix: 0.86 (0.21), residues: 563 sheet: -2.98 (0.21), residues: 543 loop : -2.25 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 261 TYR 0.023 0.002 TYR D 203 PHE 0.032 0.002 PHE C 234 TRP 0.041 0.002 TRP F 289 HIS 0.006 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (16385) covalent geometry : angle 0.67839 / 0.35 (22517) SS BOND : bond 0.00411 / 0.18 ( 6) SS BOND : angle 2.05145 / 1.09 ( 12) hydrogen bonds : bond 0.04025 / 2.81 ( 662) hydrogen bonds : angle 4.72826 / 3.24 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7183 (t80) REVERT: A 330 VAL cc_start: 0.8124 (t) cc_final: 0.7881 (t) REVERT: B 308 MET cc_start: 0.8708 (ppp) cc_final: 0.8145 (ppp) REVERT: B 309 ILE cc_start: 0.8640 (pt) cc_final: 0.8369 (pt) REVERT: C 167 MET cc_start: 0.7411 (tpt) cc_final: 0.7175 (tpt) REVERT: F 95 ASP cc_start: 0.8451 (t0) cc_final: 0.8052 (t70) REVERT: F 181 ARG cc_start: 0.6807 (tpm170) cc_final: 0.6540 (tpm170) outliers start: 34 outliers final: 31 residues processed: 192 average time/residue: 0.0982 time to fit residues: 30.1631 Evaluate side-chains 196 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 70 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.139054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095431 restraints weight = 35786.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.096291 restraints weight = 30931.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.097479 restraints weight = 25647.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.097415 restraints weight = 24555.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.097412 restraints weight = 23445.740| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16391 Z= 0.122 Angle : 0.626 14.278 22529 Z= 0.311 Chirality : 0.040 0.230 2517 Planarity : 0.004 0.048 2553 Dihedral : 17.473 179.197 3065 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.77 % Allowed : 19.87 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.13 (0.21), residues: 1711 helix: 0.99 (0.21), residues: 559 sheet: -2.82 (0.21), residues: 535 loop : -2.20 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.038 0.001 TYR F 158 PHE 0.039 0.002 PHE C 234 TRP 0.045 0.002 TRP B 306 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16385) covalent geometry : angle 0.62548 / 0.31 (22517) SS BOND : bond 0.00131 / 0.08 ( 6) SS BOND : angle 1.40550 / 0.74 ( 12) hydrogen bonds : bond 0.03566 / 2.46 ( 662) hydrogen bonds : angle 4.57385 / 3.14 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7242 (t80) REVERT: A 330 VAL cc_start: 0.8067 (t) cc_final: 0.7768 (t) REVERT: B 308 MET cc_start: 0.8714 (ppp) cc_final: 0.8148 (ppp) REVERT: B 309 ILE cc_start: 0.8511 (pt) cc_final: 0.8286 (pt) REVERT: D 167 MET cc_start: 0.7039 (tpp) cc_final: 0.6726 (tpp) REVERT: D 297 ILE cc_start: 0.8752 (mm) cc_final: 0.8398 (tt) REVERT: F 95 ASP cc_start: 0.8395 (t0) cc_final: 0.7956 (t70) REVERT: F 181 ARG cc_start: 0.6791 (tpm170) cc_final: 0.6573 (tpm170) outliers start: 28 outliers final: 26 residues processed: 191 average time/residue: 0.0966 time to fit residues: 29.5414 Evaluate side-chains 197 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 154 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 172 optimal weight: 50.0000 chunk 133 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.139373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094803 restraints weight = 35633.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.096323 restraints weight = 28284.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.097397 restraints weight = 24264.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.097901 restraints weight = 21988.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.098552 restraints weight = 20742.713| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16391 Z= 0.124 Angle : 0.633 14.834 22529 Z= 0.312 Chirality : 0.040 0.223 2517 Planarity : 0.004 0.048 2553 Dihedral : 17.446 179.039 3065 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.89 % Allowed : 20.38 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.07 (0.21), residues: 1711 helix: 0.99 (0.21), residues: 561 sheet: -2.77 (0.21), residues: 533 loop : -2.14 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.013 0.001 TYR C 112 PHE 0.037 0.001 PHE C 234 TRP 0.042 0.002 TRP E 332 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (16385) covalent geometry : angle 0.63175 / 0.31 (22517) SS BOND : bond 0.00302 / 0.15 ( 6) SS BOND : angle 1.97054 / 1.14 ( 12) hydrogen bonds : bond 0.03511 / 2.41 ( 662) hydrogen bonds : angle 4.50804 / 3.09 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2609.68 seconds wall clock time: 45 minutes 58.32 seconds (2758.32 seconds total)