Starting phenix.real_space_refine on Sat Jun 14 02:33:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8e_34544/06_2025/8h8e_34544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8e_34544/06_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_34544/06_2025/8h8e_34544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8e_34544/06_2025/8h8e_34544.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8e_34544/06_2025/8h8e_34544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8e_34544/06_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-5710/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: 11.16, per 1000 atoms: 0.71 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: 3.91 Conformation dependent library (CDL) restraints added in 1.9 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: 5.92 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: 6.27 Time building geometry restraints manager: 4.66 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: 6.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.920 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.890 ------------------------------------------------------------------------------- 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 : 1.681 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: 0.2551 time to fit residues: 91.3241 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 : 1.834 ------------------------------------------------------------------------------- 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 = 0.137913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.094418 restraints weight = 35885.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.095630 restraints weight = 28966.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095637 restraints weight = 24443.554| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- 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 1.69795 ( 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 : 2.163 Fit side-chains revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7167 (t80) REVERT: B 308 MET cc_start: 0.8843 (ppp) cc_final: 0.8279 (ppp) REVERT: D 317 LEU cc_start: 0.8375 (mp) cc_final: 0.8083 (mp) REVERT: E 66 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7763 (t80) REVERT: F 95 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8071 (t0) outliers start: 21 outliers final: 13 residues processed: 211 average time/residue: 0.2833 time to fit residues: 92.9845 Evaluate side-chains 191 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 95 ASP Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 110 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.135226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.092780 restraints weight = 35948.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092679 restraints weight = 32662.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092742 restraints weight = 30208.754| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1606 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= 0.235 Angle : 0.650 13.650 22529 Z= 0.339 Chirality : 0.042 0.201 2517 Planarity : 0.005 0.046 2553 Dihedral : 17.634 179.104 3065 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.46 % Favored : 89.48 % Rotamer: Outliers : 2.40 % Allowed : 14.38 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: -2.45 (0.21), residues: 1711 helix: 0.87 (0.21), residues: 561 sheet: -3.19 (0.20), residues: 542 loop : -2.31 (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 0.030 0.002 PHE C 238 TYR 0.027 0.002 TYR A 203 ARG 0.005 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 662) hydrogen bonds : angle 5.07439 ( 1893) SS BOND : bond 0.00368 ( 6) SS BOND : angle 1.92301 ( 12) covalent geometry : bond 0.00531 (16385) covalent geometry : angle 0.64887 (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 219 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7195 (t80) REVERT: B 308 MET cc_start: 0.8743 (ppp) cc_final: 0.8276 (ppp) outliers start: 38 outliers final: 28 residues processed: 202 average time/residue: 0.2632 time to fit residues: 84.1241 Evaluate side-chains 198 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.917 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain A residue 202 ASP 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 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 285 VAL Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 267 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 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: 3.9990 chunk 115 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 172 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN ** F 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.134377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.093065 restraints weight = 36329.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.092328 restraints weight = 31991.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.092816 restraints weight = 32077.987| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16391 Z= 0.247 Angle : 0.659 14.406 22529 Z= 0.343 Chirality : 0.042 0.221 2517 Planarity : 0.005 0.047 2553 Dihedral : 17.681 179.586 3065 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 3.41 % Allowed : 16.40 % Favored : 80.19 % 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: -2.49 (0.21), residues: 1711 helix: 0.93 (0.21), residues: 550 sheet: -3.22 (0.20), residues: 544 loop : -2.38 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 133 HIS 0.006 0.001 HIS B 131 PHE 0.037 0.002 PHE C 234 TYR 0.024 0.002 TYR A 203 ARG 0.005 0.000 ARG D 239 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 662) hydrogen bonds : angle 4.95587 ( 1893) SS BOND : bond 0.00487 ( 6) SS BOND : angle 1.98036 ( 12) covalent geometry : bond 0.00561 (16385) covalent geometry : angle 0.65790 (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 232 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.6443 (m-10) cc_final: 0.5858 (m-10) REVERT: A 325 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7144 (t80) REVERT: A 330 VAL cc_start: 0.8154 (t) cc_final: 0.7903 (t) REVERT: B 308 MET cc_start: 0.8749 (ppp) cc_final: 0.8298 (ppp) REVERT: F 158 TYR cc_start: 0.5568 (m-80) cc_final: 0.5125 (m-80) REVERT: F 181 ARG cc_start: 0.6978 (tpm170) cc_final: 0.6518 (tpm170) outliers start: 54 outliers final: 35 residues processed: 217 average time/residue: 0.2431 time to fit residues: 83.6201 Evaluate side-chains 207 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 1.767 ------------------------------------------------------------------------------- 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 234 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 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 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 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 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 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 142 optimal weight: 0.0670 chunk 174 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.137104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094581 restraints weight = 36209.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.095308 restraints weight = 27423.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095360 restraints weight = 23151.768| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2034 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= 0.143 Angle : 0.612 13.934 22529 Z= 0.310 Chirality : 0.041 0.286 2517 Planarity : 0.004 0.049 2553 Dihedral : 17.569 178.682 3065 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.59 % Allowed : 18.36 % Favored : 79.05 % 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 (0.21), residues: 553 sheet: -3.04 (0.20), residues: 549 loop : -2.25 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 133 HIS 0.004 0.001 HIS D 136 PHE 0.037 0.002 PHE C 234 TYR 0.014 0.001 TYR A 158 ARG 0.008 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 662) hydrogen bonds : angle 4.70632 ( 1893) SS BOND : bond 0.00266 ( 6) SS BOND : angle 1.60744 ( 12) covalent geometry : bond 0.00321 (16385) covalent geometry : angle 0.61116 (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 229 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.6289 (m-10) cc_final: 0.6011 (m-10) REVERT: A 283 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7868 (p90) REVERT: A 325 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7195 (t80) REVERT: A 330 VAL cc_start: 0.8058 (t) cc_final: 0.7803 (t) REVERT: B 308 MET cc_start: 0.8840 (ppp) cc_final: 0.8324 (ppp) REVERT: C 113 ASP cc_start: 0.8207 (m-30) cc_final: 0.7996 (m-30) REVERT: C 235 SER cc_start: 0.7970 (t) cc_final: 0.7548 (p) REVERT: F 181 ARG cc_start: 0.7127 (tpm170) cc_final: 0.6656 (tpm170) outliers start: 41 outliers final: 31 residues processed: 216 average time/residue: 0.2924 time to fit residues: 100.7094 Evaluate side-chains 201 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 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 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 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 112 TYR 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 313 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE 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: 0.7980 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 172 optimal weight: 30.0000 chunk 75 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 ** 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 = 0.4207 r_free = 0.4207 target = 0.134949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093137 restraints weight = 36204.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093129 restraints weight = 30560.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092888 restraints weight = 29409.032| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16391 Z= 0.216 Angle : 0.649 13.044 22529 Z= 0.332 Chirality : 0.041 0.203 2517 Planarity : 0.004 0.045 2553 Dihedral : 17.617 179.494 3065 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 3.28 % Allowed : 19.68 % Favored : 77.03 % 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: -2.33 (0.21), residues: 1711 helix: 1.01 (0.21), residues: 548 sheet: -3.05 (0.21), residues: 544 loop : -2.30 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 289 HIS 0.006 0.001 HIS C 131 PHE 0.038 0.002 PHE C 234 TYR 0.022 0.002 TYR C 75 ARG 0.004 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 662) hydrogen bonds : angle 4.78871 ( 1893) SS BOND : bond 0.00348 ( 6) SS BOND : angle 1.86590 ( 12) covalent geometry : bond 0.00491 (16385) covalent geometry : angle 0.64742 (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 230 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8042 (t80) cc_final: 0.7810 (t80) REVERT: A 222 MET cc_start: 0.7315 (mtm) cc_final: 0.6825 (mtm) REVERT: A 283 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8082 (p90) REVERT: A 325 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7227 (t80) REVERT: A 330 VAL cc_start: 0.8041 (t) cc_final: 0.7823 (t) REVERT: B 308 MET cc_start: 0.8821 (ppp) cc_final: 0.8355 (ppp) REVERT: C 235 SER cc_start: 0.7899 (t) cc_final: 0.7473 (p) REVERT: F 181 ARG cc_start: 0.7048 (tpm170) cc_final: 0.6609 (tpm170) outliers start: 52 outliers final: 39 residues processed: 214 average time/residue: 0.2332 time to fit residues: 79.4737 Evaluate side-chains 211 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 235 SER 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 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 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 191 LEU 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 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 104 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 ** 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 = 0.4235 r_free = 0.4235 target = 0.136874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.093719 restraints weight = 35874.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094444 restraints weight = 30689.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094508 restraints weight = 25044.873| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16391 Z= 0.149 Angle : 0.622 14.396 22529 Z= 0.313 Chirality : 0.040 0.217 2517 Planarity : 0.004 0.047 2553 Dihedral : 17.555 178.782 3065 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.90 % Allowed : 20.88 % Favored : 76.21 % 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: -2.20 (0.21), residues: 1711 helix: 1.05 (0.21), residues: 553 sheet: -2.89 (0.21), residues: 544 loop : -2.26 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 133 HIS 0.004 0.001 HIS C 131 PHE 0.037 0.002 PHE C 234 TYR 0.027 0.001 TYR A 158 ARG 0.005 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 662) hydrogen bonds : angle 4.62830 ( 1893) SS BOND : bond 0.00259 ( 6) SS BOND : angle 1.74466 ( 12) covalent geometry : bond 0.00339 (16385) covalent geometry : angle 0.62109 (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 228 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.6073 (m-10) cc_final: 0.5543 (m-10) REVERT: A 222 MET cc_start: 0.7423 (mtm) cc_final: 0.7131 (mtm) REVERT: A 325 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7286 (t80) REVERT: A 330 VAL cc_start: 0.8058 (t) cc_final: 0.7754 (t) REVERT: B 308 MET cc_start: 0.8836 (ppp) cc_final: 0.8333 (ppp) REVERT: C 235 SER cc_start: 0.7862 (t) cc_final: 0.7455 (p) REVERT: F 181 ARG cc_start: 0.7070 (tpm170) cc_final: 0.6649 (tpm170) outliers start: 46 outliers final: 38 residues processed: 216 average time/residue: 0.2636 time to fit residues: 90.5322 Evaluate side-chains 210 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 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 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 85 LEU 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 66 PHE Chi-restraints excluded: chain E residue 97 LEU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 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 = 0.137914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093199 restraints weight = 35742.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094822 restraints weight = 32074.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095414 restraints weight = 26200.516| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2385 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= 0.129 Angle : 0.615 13.859 22529 Z= 0.306 Chirality : 0.040 0.231 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.483 178.277 3065 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.00 % Favored : 90.94 % Rotamer: Outliers : 2.97 % Allowed : 21.45 % Favored : 75.58 % 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: -2.09 (0.21), residues: 1711 helix: 1.09 (0.21), residues: 555 sheet: -2.80 (0.21), residues: 538 loop : -2.21 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP F 289 HIS 0.003 0.001 HIS A 132 PHE 0.034 0.002 PHE C 234 TYR 0.027 0.001 TYR F 158 ARG 0.004 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 662) hydrogen bonds : angle 4.52372 ( 1893) SS BOND : bond 0.00226 ( 6) SS BOND : angle 1.58459 ( 12) covalent geometry : bond 0.00294 (16385) covalent geometry : angle 0.61397 (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 230 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.5983 (m-10) cc_final: 0.5515 (m-10) REVERT: A 222 MET cc_start: 0.7363 (mtm) cc_final: 0.7040 (mtm) REVERT: A 325 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7309 (t80) REVERT: A 330 VAL cc_start: 0.7972 (t) cc_final: 0.7719 (t) REVERT: B 308 MET cc_start: 0.8737 (ppp) cc_final: 0.8273 (ppp) REVERT: C 235 SER cc_start: 0.7822 (t) cc_final: 0.7329 (p) REVERT: C 309 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8323 (tp) REVERT: F 181 ARG cc_start: 0.7009 (tpm170) cc_final: 0.6702 (tpm170) outliers start: 47 outliers final: 36 residues processed: 216 average time/residue: 0.2360 time to fit residues: 80.2278 Evaluate side-chains 209 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 18 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 172 optimal weight: 30.0000 chunk 8 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS ** C 174 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 = 0.4233 r_free = 0.4233 target = 0.137767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.096718 restraints weight = 36144.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.096782 restraints weight = 28483.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.096849 restraints weight = 26373.989| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2506 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= 0.120 Angle : 0.636 13.855 22529 Z= 0.311 Chirality : 0.040 0.371 2517 Planarity : 0.004 0.059 2553 Dihedral : 17.428 177.747 3065 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.46 % Allowed : 22.27 % Favored : 75.27 % 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: -2.09 (0.21), residues: 1711 helix: 1.00 (0.21), residues: 566 sheet: -2.75 (0.21), residues: 533 loop : -2.24 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP F 289 HIS 0.003 0.001 HIS D 340 PHE 0.033 0.001 PHE C 234 TYR 0.021 0.001 TYR C 75 ARG 0.004 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 662) hydrogen bonds : angle 4.42868 ( 1893) SS BOND : bond 0.00156 ( 6) SS BOND : angle 1.41587 ( 12) covalent geometry : bond 0.00270 (16385) covalent geometry : angle 0.63544 (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 220 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.5877 (m-10) cc_final: 0.5551 (m-10) REVERT: A 167 MET cc_start: 0.6956 (mmm) cc_final: 0.6411 (mmm) REVERT: A 222 MET cc_start: 0.7360 (mtm) cc_final: 0.7103 (mtm) REVERT: A 283 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7613 (p90) REVERT: A 325 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7202 (t80) REVERT: A 330 VAL cc_start: 0.8002 (t) cc_final: 0.7723 (t) REVERT: B 308 MET cc_start: 0.8501 (ppp) cc_final: 0.7960 (ppp) REVERT: C 309 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8268 (tp) REVERT: D 167 MET cc_start: 0.7317 (tpp) cc_final: 0.7041 (tpp) REVERT: F 181 ARG cc_start: 0.7016 (tpm170) cc_final: 0.6709 (tpm170) outliers start: 39 outliers final: 33 residues processed: 210 average time/residue: 0.2335 time to fit residues: 77.6003 Evaluate side-chains 207 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 3.573 ------------------------------------------------------------------------------- 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 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 77 LEU 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 258 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 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 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 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 325 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 95 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 152 optimal weight: 0.4980 chunk 159 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN F 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.137058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094822 restraints weight = 35999.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.095220 restraints weight = 29639.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095088 restraints weight = 26513.176| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16391 Z= 0.135 Angle : 0.634 14.555 22529 Z= 0.313 Chirality : 0.040 0.309 2517 Planarity : 0.004 0.054 2553 Dihedral : 17.427 177.850 3065 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 2.71 % Allowed : 22.46 % Favored : 74.83 % 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: -2.06 (0.21), residues: 1711 helix: 1.07 (0.21), residues: 564 sheet: -2.74 (0.21), residues: 538 loop : -2.24 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 133 HIS 0.003 0.001 HIS D 340 PHE 0.035 0.002 PHE C 234 TYR 0.028 0.001 TYR F 158 ARG 0.009 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 662) hydrogen bonds : angle 4.41325 ( 1893) SS BOND : bond 0.00218 ( 6) SS BOND : angle 1.47663 ( 12) covalent geometry : bond 0.00309 (16385) covalent geometry : angle 0.63362 (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 222 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.7397 (mtm) cc_final: 0.7140 (mtm) REVERT: A 283 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7665 (p90) REVERT: A 325 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7198 (t80) REVERT: A 330 VAL cc_start: 0.8020 (t) cc_final: 0.7729 (t) REVERT: C 235 SER cc_start: 0.7848 (t) cc_final: 0.7358 (p) REVERT: C 309 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8285 (tp) REVERT: D 297 ILE cc_start: 0.8755 (mm) cc_final: 0.8357 (tt) REVERT: F 110 ASN cc_start: 0.6799 (t0) cc_final: 0.6565 (t0) REVERT: F 181 ARG cc_start: 0.6968 (tpm170) cc_final: 0.6670 (tpm170) outliers start: 43 outliers final: 38 residues processed: 209 average time/residue: 0.2407 time to fit residues: 78.5328 Evaluate side-chains 216 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 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 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 184 LEU 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 258 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 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 97 LEU Chi-restraints excluded: chain E residue 104 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 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 325 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 16 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 0.0020 chunk 132 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** 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 = 0.4229 r_free = 0.4229 target = 0.137580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094744 restraints weight = 35992.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.095530 restraints weight = 29379.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.095623 restraints weight = 25889.345| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16391 Z= 0.129 Angle : 0.641 15.195 22529 Z= 0.314 Chirality : 0.040 0.278 2517 Planarity : 0.004 0.057 2553 Dihedral : 17.414 177.706 3065 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.59 % Allowed : 23.03 % Favored : 74.38 % 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: -2.01 (0.21), residues: 1711 helix: 1.07 (0.21), residues: 564 sheet: -2.72 (0.22), residues: 533 loop : -2.17 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 306 HIS 0.004 0.001 HIS D 340 PHE 0.033 0.001 PHE C 234 TYR 0.040 0.001 TYR A 158 ARG 0.007 0.000 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 662) hydrogen bonds : angle 4.40405 ( 1893) SS BOND : bond 0.00195 ( 6) SS BOND : angle 1.47872 ( 12) covalent geometry : bond 0.00295 (16385) covalent geometry : angle 0.64070 (22517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6799.94 seconds wall clock time: 124 minutes 23.72 seconds (7463.72 seconds total)