Starting phenix.real_space_refine on Sat May 17 12:22:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8e_34544/05_2025/8h8e_34544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8e_34544/05_2025/8h8e_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_34544/05_2025/8h8e_34544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8e_34544/05_2025/8h8e_34544.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8e_34544/05_2025/8h8e_34544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8e_34544/05_2025/8h8e_34544.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.39, per 1000 atoms: 0.66 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: 4.20 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 5.63 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: 5.53 Time building geometry restraints manager: 4.88 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: 5.440 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: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 41.780 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 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= 0.161 Angle : 0.654 10.748 22529 Z= 0.358 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 : 15.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.039 0.002 TRP C 133 HIS 0.004 0.001 HIS A 136 PHE 0.025 0.002 PHE C 198 TYR 0.026 0.001 TYR C 112 ARG 0.003 0.000 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.16239 ( 662) hydrogen bonds : angle 7.50673 ( 1893) SS BOND : bond 0.00296 ( 6) SS BOND : angle 1.37639 ( 12) covalent geometry : bond 0.00337 (16385) covalent geometry : angle 0.65358 (22517) *********************** 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 : 1.648 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: 0.2228 time to fit residues: 78.5146 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 : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.137925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094330 restraints weight = 35887.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094826 restraints weight = 30963.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.095658 restraints weight = 27352.835| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16391 Z= 0.168 Angle : 0.632 14.204 22529 Z= 0.325 Chirality : 0.040 0.176 2517 Planarity : 0.005 0.046 2553 Dihedral : 17.628 178.666 3065 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.35 % Favored : 90.59 % Rotamer: Outliers : 1.32 % Allowed : 9.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.21), residues: 1711 helix: 1.04 (0.22), residues: 546 sheet: -3.04 (0.20), residues: 532 loop : -2.25 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 133 HIS 0.005 0.001 HIS E 99 PHE 0.035 0.002 PHE C 234 TYR 0.025 0.002 TYR C 162 ARG 0.017 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 662) hydrogen bonds : angle 5.31720 ( 1893) SS BOND : bond 0.00378 ( 6) SS BOND : angle 1.69791 ( 12) covalent geometry : bond 0.00379 (16385) covalent geometry : angle 0.63143 (22517) *********************** 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 222 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7175 (t80) REVERT: B 308 MET cc_start: 0.8843 (ppp) cc_final: 0.8280 (ppp) REVERT: D 317 LEU cc_start: 0.8376 (mp) cc_final: 0.8085 (mp) REVERT: E 66 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7773 (t80) outliers start: 21 outliers final: 13 residues processed: 211 average time/residue: 0.2389 time to fit residues: 78.0848 Evaluate side-chains 191 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 110 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.135973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094724 restraints weight = 35919.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.094446 restraints weight = 29880.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094358 restraints weight = 28338.660| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16391 Z= 0.210 Angle : 0.633 13.647 22529 Z= 0.328 Chirality : 0.041 0.195 2517 Planarity : 0.005 0.046 2553 Dihedral : 17.597 178.784 3065 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.17 % Favored : 89.77 % Rotamer: Outliers : 2.15 % Allowed : 14.13 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.21), residues: 1711 helix: 0.91 (0.21), residues: 561 sheet: -3.15 (0.20), residues: 542 loop : -2.28 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 133 HIS 0.007 0.001 HIS B 131 PHE 0.029 0.002 PHE C 238 TYR 0.025 0.002 TYR C 75 ARG 0.007 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 662) hydrogen bonds : angle 5.02851 ( 1893) SS BOND : bond 0.00355 ( 6) SS BOND : angle 1.75709 ( 12) covalent geometry : bond 0.00477 (16385) covalent geometry : angle 0.63153 (22517) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.6031 (tmm) cc_final: 0.5503 (tmm) REVERT: A 325 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7166 (t80) REVERT: B 308 MET cc_start: 0.8711 (ppp) cc_final: 0.8214 (ppp) REVERT: C 167 MET cc_start: 0.7234 (tpt) cc_final: 0.6979 (tpt) REVERT: F 95 ASP cc_start: 0.8331 (t0) cc_final: 0.7812 (t0) outliers start: 34 outliers final: 26 residues processed: 203 average time/residue: 0.2378 time to fit residues: 75.8030 Evaluate side-chains 196 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE 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 179 VAL Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 285 VAL 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 219 VAL 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 325 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 172 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS E 218 GLN F 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.135487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.094129 restraints weight = 36029.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.093906 restraints weight = 30015.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.093910 restraints weight = 29247.847| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16391 Z= 0.209 Angle : 0.628 14.385 22529 Z= 0.326 Chirality : 0.041 0.201 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.594 178.985 3065 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.22 % Allowed : 15.90 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.21), residues: 1711 helix: 0.96 (0.21), residues: 557 sheet: -3.11 (0.20), residues: 542 loop : -2.30 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 289 HIS 0.006 0.001 HIS B 131 PHE 0.039 0.002 PHE C 234 TYR 0.033 0.002 TYR A 158 ARG 0.005 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 662) hydrogen bonds : angle 4.85713 ( 1893) SS BOND : bond 0.00336 ( 6) SS BOND : angle 1.84655 ( 12) covalent geometry : bond 0.00473 (16385) covalent geometry : angle 0.62676 (22517) *********************** 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 230 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7131 (t80) REVERT: A 330 VAL cc_start: 0.8097 (t) cc_final: 0.7862 (t) REVERT: B 308 MET cc_start: 0.8789 (ppp) cc_final: 0.8272 (ppp) REVERT: F 158 TYR cc_start: 0.5379 (m-80) cc_final: 0.5083 (m-80) REVERT: F 181 ARG cc_start: 0.6959 (tpm170) cc_final: 0.6517 (tpm170) outliers start: 51 outliers final: 36 residues processed: 213 average time/residue: 0.2279 time to fit residues: 77.0094 Evaluate side-chains 210 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 133 TRP 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 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 179 VAL 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 183 GLU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 289 TRP 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 97 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 142 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 154 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 147 optimal weight: 0.3980 chunk 159 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 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 = 0.4211 r_free = 0.4211 target = 0.135119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.093785 restraints weight = 36165.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.092960 restraints weight = 30565.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093000 restraints weight = 31441.893| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16391 Z= 0.209 Angle : 0.639 14.426 22529 Z= 0.329 Chirality : 0.041 0.262 2517 Planarity : 0.004 0.047 2553 Dihedral : 17.604 179.235 3065 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 3.53 % Allowed : 17.35 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.21), residues: 1711 helix: 0.96 (0.21), residues: 555 sheet: -3.06 (0.21), residues: 542 loop : -2.36 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 133 HIS 0.005 0.001 HIS B 131 PHE 0.031 0.002 PHE C 234 TYR 0.035 0.002 TYR A 158 ARG 0.006 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 662) hydrogen bonds : angle 4.81422 ( 1893) SS BOND : bond 0.00588 ( 6) SS BOND : angle 1.80649 ( 12) covalent geometry : bond 0.00474 (16385) covalent geometry : angle 0.63821 (22517) *********************** 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 238 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8556 (p90) REVERT: A 283 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8020 (p90) REVERT: A 325 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7160 (t80) REVERT: A 330 VAL cc_start: 0.8114 (t) cc_final: 0.7858 (t) REVERT: B 308 MET cc_start: 0.8735 (ppp) cc_final: 0.8226 (ppp) REVERT: F 158 TYR cc_start: 0.5565 (m-80) cc_final: 0.5345 (m-80) REVERT: F 181 ARG cc_start: 0.7025 (tpm170) cc_final: 0.6613 (tpm170) outliers start: 56 outliers final: 42 residues processed: 222 average time/residue: 0.2278 time to fit residues: 79.7891 Evaluate side-chains 216 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 133 TRP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 179 VAL 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 183 GLU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 289 TRP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 179 VAL 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 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 301 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 90 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 172 optimal weight: 30.0000 chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** 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 = 0.4256 r_free = 0.4256 target = 0.138576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095768 restraints weight = 36277.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.096175 restraints weight = 30906.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.096439 restraints weight = 26501.116| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16391 Z= 0.118 Angle : 0.595 14.027 22529 Z= 0.297 Chirality : 0.039 0.199 2517 Planarity : 0.004 0.048 2553 Dihedral : 17.470 178.019 3065 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.46 % Allowed : 19.68 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.21), residues: 1711 helix: 1.11 (0.21), residues: 554 sheet: -2.83 (0.21), residues: 537 loop : -2.22 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 133 HIS 0.004 0.001 HIS A 132 PHE 0.036 0.002 PHE C 234 TYR 0.027 0.001 TYR F 158 ARG 0.004 0.000 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 662) hydrogen bonds : angle 4.55030 ( 1893) SS BOND : bond 0.00150 ( 6) SS BOND : angle 1.38570 ( 12) covalent geometry : bond 0.00264 (16385) covalent geometry : angle 0.59388 (22517) *********************** 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 234 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7751 (p90) REVERT: A 325 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7227 (t80) REVERT: A 330 VAL cc_start: 0.8002 (t) cc_final: 0.7801 (t) REVERT: B 308 MET cc_start: 0.8790 (ppp) cc_final: 0.8349 (ppp) REVERT: C 113 ASP cc_start: 0.8179 (m-30) cc_final: 0.7978 (m-30) REVERT: C 235 SER cc_start: 0.7876 (t) cc_final: 0.7540 (p) REVERT: F 181 ARG cc_start: 0.7042 (tpm170) cc_final: 0.6622 (tpm170) outliers start: 39 outliers final: 30 residues processed: 223 average time/residue: 0.2497 time to fit residues: 86.0569 Evaluate side-chains 203 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 133 TRP 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 283 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 166 THR 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 301 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 54 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 chunk 63 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 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 = 0.4236 r_free = 0.4236 target = 0.136918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092201 restraints weight = 35647.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093207 restraints weight = 31064.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.093736 restraints weight = 26464.769| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16391 Z= 0.163 Angle : 0.626 13.470 22529 Z= 0.314 Chirality : 0.040 0.178 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.482 178.517 3065 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 3.41 % Allowed : 20.19 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.21), residues: 1711 helix: 1.11 (0.21), residues: 555 sheet: -2.84 (0.21), residues: 540 loop : -2.21 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 289 HIS 0.004 0.001 HIS C 131 PHE 0.038 0.002 PHE C 234 TYR 0.020 0.001 TYR C 75 ARG 0.003 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 662) hydrogen bonds : angle 4.58119 ( 1893) SS BOND : bond 0.00296 ( 6) SS BOND : angle 1.62392 ( 12) covalent geometry : bond 0.00372 (16385) covalent geometry : angle 0.62506 (22517) *********************** 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 234 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.7976 (t80) cc_final: 0.7696 (t80) REVERT: A 283 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7912 (p90) REVERT: A 325 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7280 (t80) REVERT: A 330 VAL cc_start: 0.8052 (t) cc_final: 0.7743 (t) REVERT: B 306 TRP cc_start: 0.7834 (m-90) cc_final: 0.7596 (m-10) REVERT: B 308 MET cc_start: 0.8817 (ppp) cc_final: 0.8284 (ppp) REVERT: C 235 SER cc_start: 0.7826 (t) cc_final: 0.7426 (p) REVERT: F 181 ARG cc_start: 0.7015 (tpm170) cc_final: 0.6627 (tpm170) outliers start: 54 outliers final: 40 residues processed: 216 average time/residue: 0.2320 time to fit residues: 79.6466 Evaluate side-chains 216 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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 133 TRP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 ILE 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 283 PHE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 191 LEU 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 167 MET Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 137 ILE 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 301 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** F 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.135588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091468 restraints weight = 35730.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093872 restraints weight = 31577.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.093438 restraints weight = 27853.998| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16391 Z= 0.208 Angle : 0.657 13.893 22529 Z= 0.332 Chirality : 0.041 0.224 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.568 179.194 3065 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.76 % Favored : 90.18 % Rotamer: Outliers : 3.09 % Allowed : 21.26 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.21), residues: 1711 helix: 1.03 (0.21), residues: 553 sheet: -2.91 (0.21), residues: 544 loop : -2.25 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 289 HIS 0.005 0.001 HIS F 131 PHE 0.036 0.002 PHE C 234 TYR 0.018 0.002 TYR F 112 ARG 0.003 0.000 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 662) hydrogen bonds : angle 4.70257 ( 1893) SS BOND : bond 0.00431 ( 6) SS BOND : angle 2.09366 ( 12) covalent geometry : bond 0.00476 (16385) covalent geometry : angle 0.65515 (22517) *********************** 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 231 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8072 (p90) REVERT: A 325 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7325 (t80) REVERT: A 330 VAL cc_start: 0.7998 (t) cc_final: 0.7755 (t) REVERT: B 308 MET cc_start: 0.8633 (ppp) cc_final: 0.8149 (ppp) REVERT: C 235 SER cc_start: 0.7887 (t) cc_final: 0.7422 (p) REVERT: C 309 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8298 (tp) outliers start: 49 outliers final: 41 residues processed: 217 average time/residue: 0.2203 time to fit residues: 75.2012 Evaluate side-chains 214 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 133 TRP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 ILE 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 283 PHE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 191 LEU 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 153 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 137 ILE 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 301 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 18 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 172 optimal weight: 30.0000 chunk 8 optimal weight: 0.1980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.138261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.094924 restraints weight = 35770.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.095786 restraints weight = 29326.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095678 restraints weight = 25378.520| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16391 Z= 0.130 Angle : 0.630 14.253 22529 Z= 0.312 Chirality : 0.040 0.227 2517 Planarity : 0.004 0.058 2553 Dihedral : 17.493 178.233 3065 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.71 % Allowed : 22.27 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1711 helix: 1.12 (0.21), residues: 555 sheet: -2.78 (0.21), residues: 538 loop : -2.15 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 289 HIS 0.003 0.001 HIS E 131 PHE 0.037 0.002 PHE C 234 TYR 0.021 0.001 TYR C 75 ARG 0.004 0.000 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 662) hydrogen bonds : angle 4.51300 ( 1893) SS BOND : bond 0.00391 ( 6) SS BOND : angle 1.59882 ( 12) covalent geometry : bond 0.00296 (16385) covalent geometry : angle 0.62913 (22517) *********************** 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 225 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7933 (p90) REVERT: A 325 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7286 (t80) REVERT: A 330 VAL cc_start: 0.7999 (t) cc_final: 0.7727 (t) REVERT: B 308 MET cc_start: 0.8835 (ppp) cc_final: 0.8329 (ppp) REVERT: B 309 ILE cc_start: 0.8610 (pt) cc_final: 0.8357 (pt) REVERT: C 177 ARG cc_start: 0.7246 (mmp80) cc_final: 0.6906 (mmp80) REVERT: C 309 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8377 (tp) REVERT: F 181 ARG cc_start: 0.7014 (tpm170) cc_final: 0.6300 (tpm170) outliers start: 43 outliers final: 34 residues processed: 215 average time/residue: 0.2573 time to fit residues: 86.1312 Evaluate side-chains 211 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 133 TRP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 ILE 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 283 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 191 LEU 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 153 THR 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 194 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 166 THR 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 301 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 95 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 131 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 = 0.4222 r_free = 0.4222 target = 0.135828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093766 restraints weight = 35852.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094163 restraints weight = 30489.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093812 restraints weight = 28124.466| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16391 Z= 0.204 Angle : 0.674 13.590 22529 Z= 0.337 Chirality : 0.042 0.322 2517 Planarity : 0.004 0.056 2553 Dihedral : 17.560 179.060 3065 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.17 % Favored : 89.77 % Rotamer: Outliers : 2.71 % Allowed : 22.40 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.21), residues: 1711 helix: 1.02 (0.21), residues: 553 sheet: -2.88 (0.21), residues: 545 loop : -2.16 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 133 HIS 0.006 0.001 HIS C 131 PHE 0.038 0.002 PHE C 234 TYR 0.016 0.002 TYR D 203 ARG 0.005 0.000 ARG F 182 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 662) hydrogen bonds : angle 4.63838 ( 1893) SS BOND : bond 0.00341 ( 6) SS BOND : angle 1.90171 ( 12) covalent geometry : bond 0.00468 (16385) covalent geometry : angle 0.67321 (22517) ********************** 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 215 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7261 (t80) REVERT: A 330 VAL cc_start: 0.8047 (t) cc_final: 0.7765 (t) REVERT: B 308 MET cc_start: 0.8661 (ppp) cc_final: 0.8233 (ppp) REVERT: C 235 SER cc_start: 0.7835 (t) cc_final: 0.7387 (p) REVERT: C 309 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8324 (tp) REVERT: F 181 ARG cc_start: 0.6941 (tpm170) cc_final: 0.6359 (tpm170) outliers start: 43 outliers final: 39 residues processed: 204 average time/residue: 0.2388 time to fit residues: 76.7643 Evaluate side-chains 209 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 133 TRP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 ILE 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 74 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 191 LEU 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 153 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 137 ILE 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 301 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 16 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 131 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.137150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092892 restraints weight = 35815.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.093778 restraints weight = 31738.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.094012 restraints weight = 26623.561| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16391 Z= 0.159 Angle : 0.651 13.296 22529 Z= 0.323 Chirality : 0.041 0.319 2517 Planarity : 0.004 0.057 2553 Dihedral : 17.540 178.661 3065 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.90 % Allowed : 22.27 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.21), residues: 1711 helix: 1.08 (0.21), residues: 550 sheet: -2.83 (0.21), residues: 542 loop : -2.12 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 289 HIS 0.004 0.001 HIS F 131 PHE 0.036 0.002 PHE C 234 TYR 0.019 0.001 TYR C 75 ARG 0.005 0.000 ARG F 182 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 662) hydrogen bonds : angle 4.55926 ( 1893) SS BOND : bond 0.00280 ( 6) SS BOND : angle 1.72275 ( 12) covalent geometry : bond 0.00365 (16385) covalent geometry : angle 0.64975 (22517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5050.72 seconds wall clock time: 89 minutes 41.41 seconds (5381.41 seconds total)