Starting phenix.real_space_refine on Fri Jul 3 18:54:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8e_34544/07_2026/8h8e_34544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8e_34544/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h8e_34544/07_2026/8h8e_34544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8e_34544/07_2026/8h8e_34544.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8e_34544/07_2026/8h8e_34544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8e_34544/07_2026/8h8e_34544.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.35, per 1000 atoms: 0.21 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: 1.05 Conformation dependent library (CDL) restraints added in 415.6 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: 1.73 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: 2.44 Time building geometry restraints manager: 1.37 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: 22136 2.15 - 4.30: 326 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=" N THR C 240 " pdb=" CA THR C 240 " pdb=" C THR C 240 " ideal model delta sigma weight residual 108.63 101.48 7.15 1.60e+00 3.91e-01 2.00e+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: 2017 0.048 - 0.095: 393 0.095 - 0.143: 90 0.143 - 0.191: 13 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.560 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- 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= 0.167 Angle : 0.654 10.748 22529 Z= 0.387 Chirality : 0.042 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 0.00337 / 0.17 (16385) covalent geometry : angle 0.65361 / 0.39 (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 : 0.476 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: 0.0968 time to fit residues: 35.0816 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 : 0.478 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.150586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.106174 restraints weight = 38969.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.107695 restraints weight = 30571.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.109020 restraints weight = 25306.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.109859 restraints weight = 22434.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.110508 restraints weight = 20799.882| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16391 Z= 0.156 Angle : 0.624 14.108 22529 Z= 0.326 Chirality : 0.040 0.183 2517 Planarity : 0.005 0.071 2553 Dihedral : 17.685 179.052 3065 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.41 % Favored : 90.53 % Rotamer: Outliers : 1.51 % Allowed : 9.65 % Favored : 88.83 % 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: 0.95 (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 0.018 0.000 ARG C 177 TYR 0.024 0.002 TYR C 162 PHE 0.039 0.002 PHE C 234 TRP 0.028 0.002 TRP C 133 HIS 0.006 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (16385) covalent geometry : angle 0.62228 / 0.33 (22517) SS BOND : bond 0.00445 / 0.24 ( 6) SS BOND : angle 1.90975 / 1.00 ( 12) hydrogen bonds : bond 0.04458 / 2.96 ( 662) hydrogen bonds : angle 5.50514 / 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 224 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7267 (t80) REVERT: A 330 VAL cc_start: 0.7836 (t) cc_final: 0.7618 (t) REVERT: B 308 MET cc_start: 0.8929 (ppp) cc_final: 0.8321 (ppp) REVERT: E 66 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7788 (t80) REVERT: E 244 MET cc_start: 0.8750 (ptp) cc_final: 0.8548 (ptt) REVERT: F 95 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.8030 (t0) outliers start: 24 outliers final: 14 residues processed: 211 average time/residue: 0.1109 time to fit residues: 36.8665 Evaluate side-chains 191 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 309 ILE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 169 HIS 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: 40.0000 chunk 29 optimal weight: 2.9990 chunk 136 optimal weight: 0.1980 chunk 172 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.137598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.092742 restraints weight = 36265.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.094619 restraints weight = 30786.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.094904 restraints weight = 26906.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.095727 restraints weight = 23966.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.095890 restraints weight = 22306.671| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 0.039 16391 Z= 0.178 Angle : 0.607 14.432 22529 Z= 0.319 Chirality : 0.040 0.174 2517 Planarity : 0.004 0.047 2553 Dihedral : 17.623 178.957 3065 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 2.02 % Allowed : 13.25 % Favored : 84.73 % 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: -2.29 (0.21), residues: 1711 helix: 0.97 (0.22), residues: 552 sheet: -3.00 (0.20), residues: 526 loop : -2.30 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 182 TYR 0.028 0.002 TYR A 158 PHE 0.026 0.002 PHE C 238 TRP 0.029 0.002 TRP C 133 HIS 0.006 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (16385) covalent geometry : angle 0.60561 / 0.32 (22517) SS BOND : bond 0.00383 / 0.20 ( 6) SS BOND : angle 1.84283 / 0.96 ( 12) hydrogen bonds : bond 0.04162 / 2.82 ( 662) hydrogen bonds : angle 5.18650 / 3.56 ( 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 220 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7181 (t80) REVERT: A 330 VAL cc_start: 0.7887 (t) cc_final: 0.7659 (t) REVERT: B 308 MET cc_start: 0.8809 (ppp) cc_final: 0.8300 (ppp) REVERT: D 152 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7759 (t) REVERT: E 66 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7606 (t80) REVERT: E 333 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7470 (ptm) outliers start: 32 outliers final: 22 residues processed: 204 average time/residue: 0.1121 time to fit residues: 36.0298 Evaluate side-chains 195 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 111 MET 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 235 SER 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: 7.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.137767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093237 restraints weight = 35976.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094768 restraints weight = 30108.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095235 restraints weight = 26183.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.095931 restraints weight = 23972.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.095945 restraints weight = 22358.550| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16391 Z= 0.163 Angle : 0.600 14.610 22529 Z= 0.310 Chirality : 0.040 0.280 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.568 178.825 3065 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 2.02 % Allowed : 14.45 % Favored : 83.53 % 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: -2.24 (0.21), residues: 1711 helix: 1.01 (0.22), residues: 559 sheet: -2.97 (0.20), residues: 530 loop : -2.27 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.022 0.002 TYR C 162 PHE 0.025 0.002 PHE C 234 TRP 0.030 0.002 TRP D 306 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (16385) covalent geometry : angle 0.59815 / 0.31 (22517) SS BOND : bond 0.00507 / 0.26 ( 6) SS BOND : angle 2.09591 / 1.15 ( 12) hydrogen bonds : bond 0.03857 / 2.64 ( 662) hydrogen bonds : angle 4.93705 / 3.40 ( 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 212 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7207 (t80) REVERT: B 308 MET cc_start: 0.8775 (ppp) cc_final: 0.8306 (ppp) REVERT: C 102 MET cc_start: 0.7540 (ptt) cc_final: 0.7334 (ptt) REVERT: E 66 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7564 (t80) REVERT: E 333 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7492 (ptm) REVERT: F 95 ASP cc_start: 0.8309 (t0) cc_final: 0.7782 (t0) REVERT: F 181 ARG cc_start: 0.6897 (tpm170) cc_final: 0.6275 (tpm170) outliers start: 32 outliers final: 23 residues processed: 198 average time/residue: 0.1111 time to fit residues: 35.0101 Evaluate side-chains 197 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 253 ASP 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 285 VAL 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 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 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: 0.9990 chunk 173 optimal weight: 40.0000 chunk 112 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.138494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.094919 restraints weight = 35951.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095982 restraints weight = 30251.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.096588 restraints weight = 25445.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.097451 restraints weight = 23774.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.097278 restraints weight = 22658.199| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1649 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= 0.135 Angle : 0.587 13.658 22529 Z= 0.302 Chirality : 0.039 0.167 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.516 178.551 3065 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.33 % Allowed : 16.03 % Favored : 81.64 % 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: -2.17 (0.21), residues: 1711 helix: 1.02 (0.21), residues: 560 sheet: -2.92 (0.21), residues: 535 loop : -2.21 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 261 TYR 0.026 0.001 TYR A 158 PHE 0.023 0.001 PHE C 234 TRP 0.033 0.002 TRP C 133 HIS 0.003 0.001 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16385) covalent geometry : angle 0.58610 / 0.30 (22517) SS BOND : bond 0.00343 / 0.18 ( 6) SS BOND : angle 1.67999 / 0.89 ( 12) hydrogen bonds : bond 0.03750 / 2.57 ( 662) hydrogen bonds : angle 4.79357 / 3.31 ( 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 223 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.6241 (m-10) cc_final: 0.5635 (m-10) REVERT: A 325 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7206 (t80) REVERT: B 308 MET cc_start: 0.8690 (ppp) cc_final: 0.8303 (ppp) REVERT: C 167 MET cc_start: 0.7376 (tpt) cc_final: 0.7079 (tpt) REVERT: E 66 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7540 (t80) REVERT: E 333 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7437 (ptm) REVERT: F 95 ASP cc_start: 0.8301 (t0) cc_final: 0.7835 (t0) REVERT: F 181 ARG cc_start: 0.6832 (tpm170) cc_final: 0.6361 (tpm170) outliers start: 37 outliers final: 29 residues processed: 207 average time/residue: 0.1088 time to fit residues: 35.9032 Evaluate side-chains 206 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 152 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER 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 111 MET 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 97 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 219 VAL 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 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: 30.0000 chunk 91 optimal weight: 7.9990 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: 0.9980 chunk 156 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4264 r_free = 0.4264 target = 0.139036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095901 restraints weight = 35769.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.096670 restraints weight = 28687.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.096714 restraints weight = 24114.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.096913 restraints weight = 24979.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.096978 restraints weight = 23788.054| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 16391 Z= 0.130 Angle : 0.590 14.212 22529 Z= 0.300 Chirality : 0.039 0.172 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.467 178.422 3065 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.65 % Allowed : 17.03 % Favored : 80.32 % 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: -2.06 (0.21), residues: 1711 helix: 1.09 (0.21), residues: 557 sheet: -2.83 (0.21), residues: 535 loop : -2.14 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 239 TYR 0.025 0.001 TYR A 158 PHE 0.022 0.002 PHE C 238 TRP 0.030 0.002 TRP C 133 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16385) covalent geometry : angle 0.58876 / 0.30 (22517) SS BOND : bond 0.00259 / 0.14 ( 6) SS BOND : angle 1.59109 / 0.83 ( 12) hydrogen bonds : bond 0.03625 / 2.48 ( 662) hydrogen bonds : angle 4.68539 / 3.24 ( 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 228 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7203 (t80) REVERT: A 330 VAL cc_start: 0.8073 (t) cc_final: 0.7839 (t) REVERT: B 308 MET cc_start: 0.8727 (ppp) cc_final: 0.8265 (ppp) REVERT: C 167 MET cc_start: 0.7492 (tpt) cc_final: 0.7197 (tpt) REVERT: E 66 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7720 (t80) REVERT: F 95 ASP cc_start: 0.8336 (t0) cc_final: 0.7840 (t0) REVERT: F 110 ASN cc_start: 0.6996 (t0) cc_final: 0.6690 (t0) REVERT: F 181 ARG cc_start: 0.7018 (tpm170) cc_final: 0.6508 (tpm170) outliers start: 42 outliers final: 29 residues processed: 214 average time/residue: 0.1073 time to fit residues: 36.9871 Evaluate side-chains 205 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 173 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 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 111 MET Chi-restraints excluded: chain C residue 267 VAL 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 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 Chi-restraints excluded: chain F residue 325 PHE 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: 0.9980 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 93 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.137484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.094950 restraints weight = 35618.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095201 restraints weight = 28709.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095227 restraints weight = 26076.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.095339 restraints weight = 25393.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.095518 restraints weight = 24859.809| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16391 Z= 0.176 Angle : 0.621 14.506 22529 Z= 0.316 Chirality : 0.040 0.169 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.477 178.820 3065 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 2.90 % Allowed : 17.92 % Favored : 79.18 % 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: 560 sheet: -2.86 (0.21), residues: 530 loop : -2.21 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.030 0.002 TYR F 112 PHE 0.046 0.002 PHE C 234 TRP 0.054 0.002 TRP F 289 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (16385) covalent geometry : angle 0.62024 / 0.32 (22517) SS BOND : bond 0.00297 / 0.15 ( 6) SS BOND : angle 1.71661 / 0.91 ( 12) hydrogen bonds : bond 0.03729 / 2.57 ( 662) hydrogen bonds : angle 4.68454 / 3.22 ( 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 225 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7144 (t80) REVERT: A 330 VAL cc_start: 0.8115 (t) cc_final: 0.7859 (t) REVERT: C 167 MET cc_start: 0.7421 (tpt) cc_final: 0.7149 (tpt) REVERT: F 95 ASP cc_start: 0.8368 (t0) cc_final: 0.7944 (t70) REVERT: F 181 ARG cc_start: 0.6986 (tpm170) cc_final: 0.6521 (tpm170) outliers start: 46 outliers final: 37 residues processed: 207 average time/residue: 0.1107 time to fit residues: 36.4378 Evaluate side-chains 205 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 153 THR Chi-restraints excluded: chain A residue 173 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 111 MET Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 222 MET 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 72 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 235 SER 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 207 SER 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: 10.0000 chunk 141 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.0070 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN F 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.140096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.096262 restraints weight = 35981.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.097391 restraints weight = 29697.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.098081 restraints weight = 24253.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.098322 restraints weight = 23880.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.098377 restraints weight = 22723.485| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16391 Z= 0.115 Angle : 0.614 15.934 22529 Z= 0.306 Chirality : 0.040 0.226 2517 Planarity : 0.004 0.047 2553 Dihedral : 17.428 178.281 3065 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.96 % Allowed : 19.31 % Favored : 78.74 % 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: -2.10 (0.21), residues: 1711 helix: 1.01 (0.21), residues: 566 sheet: -2.82 (0.21), residues: 547 loop : -2.15 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.045 0.001 TYR A 158 PHE 0.033 0.001 PHE C 234 TRP 0.034 0.002 TRP F 289 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (16385) covalent geometry : angle 0.61366 / 0.31 (22517) SS BOND : bond 0.00240 / 0.14 ( 6) SS BOND : angle 1.40637 / 0.74 ( 12) hydrogen bonds : bond 0.03513 / 2.40 ( 662) hydrogen bonds : angle 4.56577 / 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 211 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.5952 (m-80) REVERT: A 325 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7198 (t80) REVERT: A 330 VAL cc_start: 0.8058 (t) cc_final: 0.7824 (t) REVERT: B 308 MET cc_start: 0.8806 (ppp) cc_final: 0.8155 (ppp) REVERT: C 167 MET cc_start: 0.7450 (tpt) cc_final: 0.7185 (tpt) REVERT: F 95 ASP cc_start: 0.8348 (t0) cc_final: 0.7868 (t0) REVERT: F 177 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7393 (tpp-160) REVERT: F 181 ARG cc_start: 0.6908 (tpm170) cc_final: 0.6484 (tpm170) outliers start: 31 outliers final: 27 residues processed: 201 average time/residue: 0.1175 time to fit residues: 36.6565 Evaluate side-chains 198 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 158 TYR 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 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 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 85 LEU Chi-restraints excluded: chain E residue 194 THR 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 301 ILE Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 112 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.137730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093505 restraints weight = 35924.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094412 restraints weight = 31517.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.095071 restraints weight = 25999.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.094568 restraints weight = 28018.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094847 restraints weight = 26540.332| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16391 Z= 0.179 Angle : 0.649 15.778 22529 Z= 0.327 Chirality : 0.041 0.353 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.457 178.808 3065 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 2.27 % Allowed : 19.68 % Favored : 78.04 % 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: -2.14 (0.21), residues: 1711 helix: 0.98 (0.21), residues: 561 sheet: -2.85 (0.21), residues: 540 loop : -2.16 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.022 0.002 TYR C 75 PHE 0.031 0.002 PHE C 234 TRP 0.046 0.002 TRP B 306 HIS 0.004 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (16385) covalent geometry : angle 0.64835 / 0.33 (22517) SS BOND : bond 0.00300 / 0.14 ( 6) SS BOND : angle 1.67678 / 0.88 ( 12) hydrogen bonds : bond 0.03698 / 2.53 ( 662) hydrogen bonds : angle 4.62914 / 3.18 ( 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 210 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7198 (t80) REVERT: A 330 VAL cc_start: 0.8080 (t) cc_final: 0.7795 (t) REVERT: B 308 MET cc_start: 0.8786 (ppp) cc_final: 0.8145 (ppp) REVERT: C 167 MET cc_start: 0.7449 (tpt) cc_final: 0.7175 (tpt) REVERT: F 95 ASP cc_start: 0.8352 (t0) cc_final: 0.7967 (t70) REVERT: F 177 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7338 (tpp-160) REVERT: F 181 ARG cc_start: 0.6879 (tpm170) cc_final: 0.6473 (tpm170) outliers start: 36 outliers final: 29 residues processed: 196 average time/residue: 0.1133 time to fit residues: 35.1598 Evaluate side-chains 198 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 153 THR 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 111 MET 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 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: 3.9990 chunk 155 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.138532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094806 restraints weight = 35917.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.095543 restraints weight = 30753.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.096052 restraints weight = 25954.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.096223 restraints weight = 26285.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.096280 restraints weight = 24538.318| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16391 Z= 0.150 Angle : 0.632 15.457 22529 Z= 0.317 Chirality : 0.041 0.337 2517 Planarity : 0.004 0.050 2553 Dihedral : 17.457 178.800 3065 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 1.96 % Allowed : 20.32 % 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: -2.09 (0.21), residues: 1711 helix: 1.02 (0.21), residues: 559 sheet: -2.83 (0.21), residues: 540 loop : -2.11 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.033 0.001 TYR F 158 PHE 0.031 0.002 PHE C 234 TRP 0.042 0.002 TRP C 133 HIS 0.003 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (16385) covalent geometry : angle 0.63087 / 0.32 (22517) SS BOND : bond 0.00232 / 0.12 ( 6) SS BOND : angle 1.62728 / 0.87 ( 12) hydrogen bonds : bond 0.03578 / 2.45 ( 662) hydrogen bonds : angle 4.57959 / 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 207 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7223 (t80) REVERT: A 330 VAL cc_start: 0.8039 (t) cc_final: 0.7768 (t) REVERT: B 308 MET cc_start: 0.8771 (ppp) cc_final: 0.8184 (ppp) REVERT: B 309 ILE cc_start: 0.8520 (pt) cc_final: 0.8297 (pt) REVERT: D 167 MET cc_start: 0.7142 (tpp) cc_final: 0.6797 (tpp) REVERT: F 95 ASP cc_start: 0.8402 (t0) cc_final: 0.7872 (t0) REVERT: F 181 ARG cc_start: 0.6881 (tpm170) cc_final: 0.6500 (tpm170) REVERT: F 222 MET cc_start: 0.7812 (tmm) cc_final: 0.7570 (tmm) outliers start: 31 outliers final: 28 residues processed: 197 average time/residue: 0.1108 time to fit residues: 34.5458 Evaluate side-chains 197 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 153 THR 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 71 LEU 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 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 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: 0.9990 chunk 75 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 172 optimal weight: 40.0000 chunk 133 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.139135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.094550 restraints weight = 35465.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.097271 restraints weight = 29754.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.096734 restraints weight = 25255.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.097368 restraints weight = 24061.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.097664 restraints weight = 22724.535| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16391 Z= 0.129 Angle : 0.639 14.606 22529 Z= 0.318 Chirality : 0.041 0.317 2517 Planarity : 0.004 0.048 2553 Dihedral : 17.446 178.588 3065 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.02 % Allowed : 20.76 % Favored : 77.22 % 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: -2.11 (0.21), residues: 1711 helix: 1.00 (0.21), residues: 565 sheet: -2.83 (0.21), residues: 539 loop : -2.18 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.025 0.001 TYR A 158 PHE 0.031 0.001 PHE C 234 TRP 0.043 0.002 TRP B 306 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16385) covalent geometry : angle 0.63840 / 0.32 (22517) SS BOND : bond 0.00225 / 0.12 ( 6) SS BOND : angle 1.49208 / 0.80 ( 12) hydrogen bonds : bond 0.03530 / 2.41 ( 662) hydrogen bonds : angle 4.54837 / 3.12 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2914.89 seconds wall clock time: 51 minutes 20.91 seconds (3080.91 seconds total)