Starting phenix.real_space_refine on Sun Aug 24 00:18:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8e_34544/08_2025/8h8e_34544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8e_34544/08_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_34544/08_2025/8h8e_34544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8e_34544/08_2025/8h8e_34544.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8e_34544/08_2025/8h8e_34544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8e_34544/08_2025/8h8e_34544.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 78 5.16 5 C 9962 2.51 5 N 2662 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15818 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2366 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 275} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2337 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain: "C" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2351 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2425 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain: "E" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2392 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 12, 'TRANS': 276} Chain: "F" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2354 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "G" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1593 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 28, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 58} Time building chain proxies: 4.01, per 1000 atoms: 0.25 Number of scatterers: 15818 At special positions: 0 Unit cell: (96.28, 151.06, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 74 15.00 O 3042 8.00 N 2662 7.00 C 9962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 151 " distance=2.03 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 151 " distance=2.03 Simple disulfide: pdb=" SG CYS F 129 " - pdb=" SG CYS F 151 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 603.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3326 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 29 sheets defined 34.9% alpha, 23.9% beta 22 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 56 through 99 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.986A pdb=" N CYS A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 343 Processing helix chain 'B' and resid 61 through 99 removed outlier: 3.778A pdb=" N LEU B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 334 Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.804A pdb=" N HIS B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 69 through 99 removed outlier: 3.597A pdb=" N TYR C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.651A pdb=" N LYS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 226 removed outlier: 3.738A pdb=" N MET C 222 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 226 " --> pdb=" O MET C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 345 Processing helix chain 'D' and resid 59 through 99 removed outlier: 3.854A pdb=" N ASN D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL D 83 " --> pdb=" O MET D 79 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.789A pdb=" N MET D 222 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 304 through 349 removed outlier: 3.797A pdb=" N MET D 308 " --> pdb=" O ASN D 304 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 99 removed outlier: 3.759A pdb=" N SER E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET E 79 " --> pdb=" O TYR E 75 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE E 84 " --> pdb=" O GLY E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.548A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 229 removed outlier: 3.556A pdb=" N MET E 222 " --> pdb=" O GLN E 218 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 226 " --> pdb=" O MET E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 4.415A pdb=" N LYS E 278 " --> pdb=" O THR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 342 removed outlier: 3.969A pdb=" N ALA E 310 " --> pdb=" O TRP E 306 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG E 337 " --> pdb=" O MET E 333 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG E 338 " --> pdb=" O ILE E 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS E 342 " --> pdb=" O ARG E 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 96 removed outlier: 3.880A pdb=" N LEU F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 71 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE F 72 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'F' and resid 217 through 229 removed outlier: 3.738A pdb=" N CYS F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 227 " --> pdb=" O GLN F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 342 removed outlier: 3.649A pdb=" N MET F 308 " --> pdb=" O ASN F 304 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU F 317 " --> pdb=" O CYS F 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 331 " --> pdb=" O LYS F 327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108 removed outlier: 3.621A pdb=" N ILE A 294 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 285 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 287 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 186 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N HIS A 190 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 126 " --> pdb=" O HIS A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 108 removed outlier: 3.621A pdb=" N ILE A 294 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE A 238 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL A 286 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 240 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLU A 288 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL A 242 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS A 290 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N MET A 244 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N LEU A 246 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A 294 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LYS A 248 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 296 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS A 250 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLN A 298 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 243 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 263 " --> pdb=" O LYS A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 158 removed outlier: 3.791A pdb=" N ILE A 172 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 156 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 119 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 173 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 201 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 234 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 232 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 104 removed outlier: 8.193A pdb=" N TYR B 293 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 246 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 295 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 299 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP B 241 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 243 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 108 removed outlier: 8.193A pdb=" N TYR B 293 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 246 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 295 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 299 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 286 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 119 removed outlier: 3.535A pdb=" N PHE B 234 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.589A pdb=" N ARG B 125 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 190 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 281 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 159 removed outlier: 3.631A pdb=" N ILE B 156 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 101 through 108 removed outlier: 6.471A pdb=" N LEU C 246 " --> pdb=" O GLN C 295 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE C 297 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LYS C 248 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP C 299 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS C 250 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 117 removed outlier: 3.636A pdb=" N PHE C 206 " --> pdb=" O GLY C 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 126 through 132 removed outlier: 6.213A pdb=" N GLN C 188 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS C 129 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE C 186 " --> pdb=" O CYS C 129 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N HIS C 131 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 184 " --> pdb=" O HIS C 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.844A pdb=" N ILE C 172 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 158 through 159 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB7, first strand: chain 'C' and resid 264 through 265 removed outlier: 3.718A pdb=" N TRP C 241 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR C 240 " --> pdb=" O VAL C 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 105 removed outlier: 9.924A pdb=" N GLN D 295 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 246 " --> pdb=" O GLN D 295 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE D 297 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS D 248 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR D 240 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU D 288 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL D 242 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN D 281 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 191 " --> pdb=" O GLN D 281 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 285 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN D 188 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS D 190 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 103 through 105 removed outlier: 9.924A pdb=" N GLN D 295 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 246 " --> pdb=" O GLN D 295 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE D 297 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS D 248 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 243 " --> pdb=" O GLU D 263 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 257 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 173 through 174 removed outlier: 3.505A pdb=" N PHE D 234 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP D 232 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 158 through 159 removed outlier: 3.946A pdb=" N TYR D 158 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 168 " --> pdb=" O TYR D 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 101 through 108 removed outlier: 3.944A pdb=" N SER E 105 " --> pdb=" O GLU E 296 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 296 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 14.566A pdb=" N TYR E 293 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N MET E 244 " --> pdb=" O TYR E 293 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N GLN E 295 " --> pdb=" O MET E 244 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU E 246 " --> pdb=" O GLN E 295 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE E 297 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS E 248 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASP E 299 " --> pdb=" O LYS E 248 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS E 243 " --> pdb=" O GLU E 263 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR E 249 " --> pdb=" O SER E 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 101 through 108 removed outlier: 3.944A pdb=" N SER E 105 " --> pdb=" O GLU E 296 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 296 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 14.566A pdb=" N TYR E 293 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N MET E 244 " --> pdb=" O TYR E 293 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N GLN E 295 " --> pdb=" O MET E 244 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU E 246 " --> pdb=" O GLN E 295 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE E 297 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS E 248 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASP E 299 " --> pdb=" O LYS E 248 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU E 288 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 118 through 120 removed outlier: 4.108A pdb=" N ASP E 202 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC7, first strand: chain 'F' and resid 100 through 107 removed outlier: 3.567A pdb=" N GLN F 295 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 259 " --> pdb=" O VAL F 247 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 100 through 107 removed outlier: 3.567A pdb=" N GLN F 295 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 117 through 120 removed outlier: 4.017A pdb=" N ASP F 202 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AD2, first strand: chain 'F' and resid 239 through 240 636 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4665 1.34 - 1.46: 3968 1.46 - 1.58: 7478 1.58 - 1.70: 148 1.70 - 1.82: 126 Bond restraints: 16385 Sorted by residual: bond pdb=" C ASP F 197 " pdb=" N PHE F 198 " ideal model delta sigma weight residual 1.331 1.292 0.039 1.34e-02 5.57e+03 8.29e+00 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.78e+00 bond pdb=" N LEU A 77 " pdb=" CA LEU A 77 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.21e+00 bond pdb=" N LEU A 73 " pdb=" CA LEU A 73 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.02e+00 bond pdb=" N LEU F 71 " pdb=" CA LEU F 71 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 5.13e+00 ... (remaining 16380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 22136 2.15 - 4.30: 326 4.30 - 6.45: 39 6.45 - 8.60: 13 8.60 - 10.75: 3 Bond angle restraints: 22517 Sorted by residual: angle pdb=" N TYR C 112 " pdb=" CA TYR C 112 " pdb=" C TYR C 112 " ideal model delta sigma weight residual 111.02 121.77 -10.75 1.22e+00 6.72e-01 7.76e+01 angle pdb=" N MET C 111 " pdb=" CA MET C 111 " pdb=" C MET C 111 " ideal model delta sigma weight residual 108.23 116.66 -8.43 1.38e+00 5.25e-01 3.73e+01 angle pdb=" N HIS A 132 " pdb=" CA HIS A 132 " pdb=" C HIS A 132 " ideal model delta sigma weight residual 109.15 100.39 8.76 1.44e+00 4.82e-01 3.70e+01 angle pdb=" N TRP A 133 " pdb=" CA TRP A 133 " pdb=" C TRP A 133 " ideal model delta sigma weight residual 110.17 101.71 8.46 1.61e+00 3.86e-01 2.76e+01 angle pdb=" N THR C 240 " pdb=" CA THR C 240 " pdb=" C THR C 240 " ideal model delta sigma weight residual 108.63 101.48 7.15 1.60e+00 3.91e-01 2.00e+01 ... (remaining 22512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 9526 35.43 - 70.85: 354 70.85 - 106.28: 44 106.28 - 141.70: 2 141.70 - 177.13: 3 Dihedral angle restraints: 9929 sinusoidal: 4821 harmonic: 5108 Sorted by residual: dihedral pdb=" O4' C G 74 " pdb=" C1' C G 74 " pdb=" N1 C G 74 " pdb=" C2 C G 74 " ideal model delta sinusoidal sigma weight residual -128.00 49.13 -177.13 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CB CYS E 129 " pdb=" SG CYS E 129 " pdb=" SG CYS E 151 " pdb=" CB CYS E 151 " ideal model delta sinusoidal sigma weight residual 93.00 23.89 69.11 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CB CYS D 129 " pdb=" SG CYS D 129 " pdb=" SG CYS D 151 " pdb=" CB CYS D 151 " ideal model delta sinusoidal sigma weight residual 93.00 29.59 63.41 1 1.00e+01 1.00e-02 5.30e+01 ... (remaining 9926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2017 0.048 - 0.095: 393 0.095 - 0.143: 90 0.143 - 0.191: 13 0.191 - 0.239: 4 Chirality restraints: 2517 Sorted by residual: chirality pdb=" CB ILE A 201 " pdb=" CA ILE A 201 " pdb=" CG1 ILE A 201 " pdb=" CG2 ILE A 201 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP A 197 " pdb=" N ASP A 197 " pdb=" C ASP A 197 " pdb=" CB ASP A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA TYR C 112 " pdb=" N TYR C 112 " pdb=" C TYR C 112 " pdb=" CB TYR C 112 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2514 not shown) Planarity restraints: 2553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 158 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C TYR A 158 " 0.047 2.00e-02 2.50e+03 pdb=" O TYR A 158 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE A 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 133 " -0.015 2.00e-02 2.50e+03 1.47e-02 5.42e+00 pdb=" CG TRP C 133 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 133 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 133 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 133 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 133 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 133 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 133 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 133 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 133 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 142 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO D 143 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 143 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 143 " 0.030 5.00e-02 4.00e+02 ... (remaining 2550 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1932 2.75 - 3.29: 16526 3.29 - 3.82: 27055 3.82 - 4.36: 30269 4.36 - 4.90: 49794 Nonbonded interactions: 125576 Sorted by model distance: nonbonded pdb=" O4 U G 33 " pdb=" N4 C G 38 " model vdw 2.210 3.120 nonbonded pdb=" O ASP D 224 " pdb=" OG SER D 228 " model vdw 2.229 3.040 nonbonded pdb=" O2' G G 17 " pdb=" N2 G G 56 " model vdw 2.236 3.120 nonbonded pdb=" OE2 GLU B 263 " pdb=" NZ LYS B 290 " model vdw 2.239 3.120 nonbonded pdb=" OG1 THR D 194 " pdb=" OE1 GLN D 196 " model vdw 2.243 3.040 ... (remaining 125571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 61 through 342) selection = (chain 'B' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) selection = (chain 'C' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) selection = (chain 'D' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) selection = (chain 'E' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) selection = (chain 'F' and (resid 61 through 72 or (resid 73 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 342)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.710 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- 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 : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.21), residues: 1711 helix: 0.80 (0.22), residues: 556 sheet: -3.15 (0.21), residues: 520 loop : -2.37 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.026 0.001 TYR C 112 PHE 0.025 0.002 PHE C 198 TRP 0.039 0.002 TRP C 133 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00337 (16385) covalent geometry : angle 0.65358 (22517) SS BOND : bond 0.00296 ( 6) SS BOND : angle 1.37639 ( 12) hydrogen bonds : bond 0.16239 ( 662) hydrogen bonds : angle 7.50673 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.563 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: 0.1104 time to fit residues: 39.5704 Evaluate side-chains 179 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4264 r_free = 0.4264 target = 0.138831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.094303 restraints weight = 35756.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.096865 restraints weight = 30027.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.097182 restraints weight = 23300.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.097564 restraints weight = 22801.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.097855 restraints weight = 21381.055| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16391 Z= 0.148 Angle : 0.616 14.167 22529 Z= 0.315 Chirality : 0.040 0.173 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.585 178.458 3065 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.83 % Favored : 91.12 % Rotamer: Outliers : 1.26 % Allowed : 9.59 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.21), residues: 1711 helix: 1.06 (0.22), residues: 546 sheet: -3.00 (0.21), residues: 534 loop : -2.23 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 177 TYR 0.024 0.002 TYR C 162 PHE 0.031 0.002 PHE C 234 TRP 0.027 0.002 TRP C 133 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00330 (16385) covalent geometry : angle 0.61485 (22517) SS BOND : bond 0.01391 ( 6) SS BOND : angle 1.57904 ( 12) hydrogen bonds : bond 0.03785 ( 662) hydrogen bonds : angle 5.23520 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7205 (t80) REVERT: B 308 MET cc_start: 0.8818 (ppp) cc_final: 0.8254 (ppp) REVERT: C 111 MET cc_start: 0.5842 (mmm) cc_final: 0.4997 (tpp) REVERT: D 317 LEU cc_start: 0.8347 (mp) cc_final: 0.8062 (mp) REVERT: E 66 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7815 (t80) outliers start: 20 outliers final: 13 residues processed: 209 average time/residue: 0.1117 time to fit residues: 36.6443 Evaluate side-chains 192 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 285 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 174 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 172 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** F 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.138741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.095284 restraints weight = 36185.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.096044 restraints weight = 30261.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.096372 restraints weight = 25831.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.096440 restraints weight = 26690.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.096668 restraints weight = 24482.738| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1557 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= 0.138 Angle : 0.585 14.002 22529 Z= 0.300 Chirality : 0.039 0.166 2517 Planarity : 0.004 0.046 2553 Dihedral : 17.463 177.705 3065 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.59 % Favored : 91.35 % Rotamer: Outliers : 1.96 % Allowed : 13.25 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.21), residues: 1711 helix: 1.09 (0.21), residues: 559 sheet: -2.89 (0.21), residues: 526 loop : -2.20 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.023 0.001 TYR F 158 PHE 0.026 0.001 PHE C 234 TRP 0.032 0.002 TRP C 133 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00310 (16385) covalent geometry : angle 0.58414 (22517) SS BOND : bond 0.00185 ( 6) SS BOND : angle 1.49941 ( 12) hydrogen bonds : bond 0.03544 ( 662) hydrogen bonds : angle 4.78560 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7731 (tpp) cc_final: 0.7475 (tpp) REVERT: A 325 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7239 (t80) REVERT: B 308 MET cc_start: 0.8803 (ppp) cc_final: 0.8302 (ppp) REVERT: E 66 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7523 (t80) REVERT: E 333 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7416 (ptm) outliers start: 31 outliers final: 22 residues processed: 209 average time/residue: 0.1143 time to fit residues: 37.7367 Evaluate side-chains 195 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 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 291 ASP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 104 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN F 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.138434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.094697 restraints weight = 36141.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095756 restraints weight = 31052.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.096044 restraints weight = 26045.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.096446 restraints weight = 25056.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.096494 restraints weight = 24660.270| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1799 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= 0.141 Angle : 0.583 14.077 22529 Z= 0.297 Chirality : 0.039 0.271 2517 Planarity : 0.004 0.045 2553 Dihedral : 17.415 177.782 3065 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 2.33 % Allowed : 15.08 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.21), residues: 1711 helix: 1.15 (0.21), residues: 557 sheet: -2.86 (0.21), residues: 532 loop : -2.13 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.029 0.001 TYR F 158 PHE 0.034 0.002 PHE C 234 TRP 0.029 0.002 TRP F 289 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00320 (16385) covalent geometry : angle 0.58242 (22517) SS BOND : bond 0.00442 ( 6) SS BOND : angle 1.52283 ( 12) hydrogen bonds : bond 0.03400 ( 662) hydrogen bonds : angle 4.62794 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.6046 (tmm) cc_final: 0.5478 (tmm) REVERT: A 308 MET cc_start: 0.7723 (tpp) cc_final: 0.7513 (tpp) REVERT: A 325 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7193 (t80) REVERT: A 330 VAL cc_start: 0.8074 (t) cc_final: 0.7844 (t) REVERT: B 308 MET cc_start: 0.8780 (ppp) cc_final: 0.8299 (ppp) REVERT: B 309 ILE cc_start: 0.8514 (pt) cc_final: 0.8285 (pt) REVERT: C 167 MET cc_start: 0.7399 (tpt) cc_final: 0.7146 (tpt) REVERT: E 66 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7490 (t80) REVERT: E 333 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7456 (ptm) REVERT: F 181 ARG cc_start: 0.6916 (tpm170) cc_final: 0.6543 (tpm170) outliers start: 37 outliers final: 23 residues processed: 206 average time/residue: 0.1083 time to fit residues: 35.6354 Evaluate side-chains 202 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 129 optimal weight: 0.6980 chunk 173 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 133 optimal weight: 0.2980 chunk 166 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** D 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.139752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095182 restraints weight = 36073.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.097383 restraints weight = 30479.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.097982 restraints weight = 23938.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.098283 restraints weight = 23499.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098393 restraints weight = 22286.200| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1974 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= 0.119 Angle : 0.581 14.863 22529 Z= 0.291 Chirality : 0.039 0.196 2517 Planarity : 0.004 0.045 2553 Dihedral : 17.365 177.454 3065 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.65 % Allowed : 16.34 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.21), residues: 1711 helix: 1.17 (0.21), residues: 560 sheet: -2.71 (0.22), residues: 528 loop : -2.11 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.035 0.001 TYR A 158 PHE 0.026 0.001 PHE C 234 TRP 0.036 0.001 TRP C 133 HIS 0.007 0.001 HIS F 131 Details of bonding type rmsd covalent geometry : bond 0.00268 (16385) covalent geometry : angle 0.58022 (22517) SS BOND : bond 0.00217 ( 6) SS BOND : angle 1.28446 ( 12) hydrogen bonds : bond 0.03271 ( 662) hydrogen bonds : angle 4.49505 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7758 (tpp) cc_final: 0.7543 (tpp) REVERT: A 325 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7206 (t80) REVERT: A 330 VAL cc_start: 0.8052 (t) cc_final: 0.7807 (t) REVERT: B 308 MET cc_start: 0.8703 (ppp) cc_final: 0.8267 (ppp) REVERT: B 309 ILE cc_start: 0.8502 (pt) cc_final: 0.8257 (pt) REVERT: C 167 MET cc_start: 0.7352 (tpt) cc_final: 0.7132 (tpt) REVERT: D 297 ILE cc_start: 0.8706 (mm) cc_final: 0.8394 (tt) REVERT: E 66 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7500 (t80) REVERT: F 95 ASP cc_start: 0.8297 (t0) cc_final: 0.7698 (t0) REVERT: F 181 ARG cc_start: 0.6771 (tpm170) cc_final: 0.6552 (tpm170) REVERT: F 222 MET cc_start: 0.7694 (tmm) cc_final: 0.7136 (tmm) REVERT: F 256 GLN cc_start: 0.8061 (tt0) cc_final: 0.7821 (tm-30) outliers start: 42 outliers final: 26 residues processed: 217 average time/residue: 0.1143 time to fit residues: 39.2197 Evaluate side-chains 204 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 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 289 TRP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 171 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** D 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.137037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093620 restraints weight = 35710.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.094775 restraints weight = 29287.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.094987 restraints weight = 24885.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095270 restraints weight = 25681.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.095273 restraints weight = 24017.930| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16391 Z= 0.186 Angle : 0.618 13.026 22529 Z= 0.315 Chirality : 0.040 0.206 2517 Planarity : 0.004 0.045 2553 Dihedral : 17.449 178.518 3065 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 2.84 % Allowed : 18.42 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.21), residues: 1711 helix: 1.23 (0.21), residues: 550 sheet: -2.83 (0.21), residues: 539 loop : -2.12 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 239 TYR 0.022 0.002 TYR C 75 PHE 0.035 0.002 PHE C 234 TRP 0.040 0.002 TRP C 133 HIS 0.005 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00420 (16385) covalent geometry : angle 0.61688 (22517) SS BOND : bond 0.00307 ( 6) SS BOND : angle 1.67763 ( 12) hydrogen bonds : bond 0.03511 ( 662) hydrogen bonds : angle 4.58176 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 330 VAL cc_start: 0.8054 (t) cc_final: 0.7844 (t) REVERT: B 308 MET cc_start: 0.8764 (ppp) cc_final: 0.8330 (ppp) REVERT: B 309 ILE cc_start: 0.8619 (pt) cc_final: 0.8340 (pt) REVERT: C 167 MET cc_start: 0.7458 (tpt) cc_final: 0.7225 (tpt) REVERT: C 174 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: D 297 ILE cc_start: 0.8728 (mm) cc_final: 0.8427 (tt) REVERT: F 95 ASP cc_start: 0.8436 (t0) cc_final: 0.7837 (t0) REVERT: F 181 ARG cc_start: 0.6933 (tpm170) cc_final: 0.6590 (tpm170) outliers start: 45 outliers final: 35 residues processed: 213 average time/residue: 0.1103 time to fit residues: 36.8755 Evaluate side-chains 211 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 247 VAL 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 174 GLN 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 267 VAL Chi-restraints excluded: chain C residue 289 TRP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 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 16 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 55 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** 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 = 0.137403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095109 restraints weight = 35848.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.095703 restraints weight = 29260.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095535 restraints weight = 26081.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095644 restraints weight = 26515.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.095700 restraints weight = 26093.021| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2242 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= 0.129 Angle : 0.587 13.391 22529 Z= 0.295 Chirality : 0.039 0.249 2517 Planarity : 0.004 0.045 2553 Dihedral : 17.411 177.925 3065 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.78 % Allowed : 19.68 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.21), residues: 1711 helix: 1.22 (0.21), residues: 555 sheet: -2.73 (0.21), residues: 533 loop : -2.15 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 177 TYR 0.028 0.001 TYR F 158 PHE 0.030 0.001 PHE C 234 TRP 0.043 0.002 TRP F 289 HIS 0.005 0.001 HIS F 131 Details of bonding type rmsd covalent geometry : bond 0.00292 (16385) covalent geometry : angle 0.58583 (22517) SS BOND : bond 0.00240 ( 6) SS BOND : angle 1.59844 ( 12) hydrogen bonds : bond 0.03267 ( 662) hydrogen bonds : angle 4.45098 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.6186 (p90) cc_final: 0.5917 (p90) REVERT: A 167 MET cc_start: 0.7099 (mmm) cc_final: 0.6362 (mmp) REVERT: A 283 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7692 (p90) REVERT: A 325 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7156 (t80) REVERT: A 330 VAL cc_start: 0.8073 (t) cc_final: 0.7764 (t) REVERT: B 308 MET cc_start: 0.8561 (ppp) cc_final: 0.8137 (ppp) REVERT: B 309 ILE cc_start: 0.8577 (pt) cc_final: 0.8278 (pt) REVERT: C 167 MET cc_start: 0.7272 (tpt) cc_final: 0.7069 (tpt) REVERT: C 174 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: D 297 ILE cc_start: 0.8747 (mm) cc_final: 0.8410 (tt) REVERT: F 95 ASP cc_start: 0.8368 (t0) cc_final: 0.7790 (t0) REVERT: F 181 ARG cc_start: 0.6893 (tpm170) cc_final: 0.6601 (tpm170) REVERT: F 256 GLN cc_start: 0.8058 (tt0) cc_final: 0.7823 (tm-30) outliers start: 44 outliers final: 36 residues processed: 221 average time/residue: 0.1034 time to fit residues: 36.2054 Evaluate side-chains 217 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 71 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 174 GLN Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 TRP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.0170 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- 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 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.137742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.095219 restraints weight = 36134.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095668 restraints weight = 29500.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.095345 restraints weight = 27050.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.095728 restraints weight = 27683.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095842 restraints weight = 25692.499| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2354 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= 0.124 Angle : 0.595 12.988 22529 Z= 0.297 Chirality : 0.039 0.215 2517 Planarity : 0.004 0.045 2553 Dihedral : 17.385 177.735 3065 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.84 % Allowed : 20.38 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.21), residues: 1711 helix: 1.23 (0.21), residues: 559 sheet: -2.74 (0.21), residues: 538 loop : -2.13 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.015 0.001 TYR F 158 PHE 0.033 0.001 PHE C 234 TRP 0.047 0.002 TRP C 133 HIS 0.004 0.001 HIS F 131 Details of bonding type rmsd covalent geometry : bond 0.00281 (16385) covalent geometry : angle 0.59389 (22517) SS BOND : bond 0.00224 ( 6) SS BOND : angle 1.49944 ( 12) hydrogen bonds : bond 0.03234 ( 662) hydrogen bonds : angle 4.38959 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7684 (p90) REVERT: A 325 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7199 (t80) REVERT: A 330 VAL cc_start: 0.8011 (t) cc_final: 0.7761 (t) REVERT: C 174 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: D 297 ILE cc_start: 0.8726 (mm) cc_final: 0.8394 (tt) REVERT: E 66 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7725 (t80) REVERT: F 95 ASP cc_start: 0.8365 (t0) cc_final: 0.7778 (t0) REVERT: F 111 MET cc_start: 0.7747 (tpp) cc_final: 0.6640 (tpp) REVERT: F 181 ARG cc_start: 0.6852 (tpm170) cc_final: 0.6596 (tpm170) REVERT: F 256 GLN cc_start: 0.8106 (tt0) cc_final: 0.7847 (tm-30) outliers start: 45 outliers final: 36 residues processed: 213 average time/residue: 0.1131 time to fit residues: 38.2257 Evaluate side-chains 216 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 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 174 GLN Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 194 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 112 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 64 optimal weight: 0.0000 chunk 116 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4222 r_free = 0.4222 target = 0.136944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094051 restraints weight = 36025.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094752 restraints weight = 30585.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.094721 restraints weight = 26502.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094845 restraints weight = 27390.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094985 restraints weight = 25563.866| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16391 Z= 0.148 Angle : 0.620 12.735 22529 Z= 0.309 Chirality : 0.040 0.199 2517 Planarity : 0.004 0.048 2553 Dihedral : 17.414 177.978 3065 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 3.03 % Allowed : 20.25 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.21), residues: 1711 helix: 1.22 (0.21), residues: 555 sheet: -2.73 (0.21), residues: 533 loop : -2.16 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 177 TYR 0.034 0.001 TYR F 158 PHE 0.032 0.002 PHE C 234 TRP 0.039 0.002 TRP C 133 HIS 0.003 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00337 (16385) covalent geometry : angle 0.61903 (22517) SS BOND : bond 0.00236 ( 6) SS BOND : angle 1.55839 ( 12) hydrogen bonds : bond 0.03296 ( 662) hydrogen bonds : angle 4.40073 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7742 (p90) REVERT: A 325 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7201 (t80) REVERT: A 330 VAL cc_start: 0.8020 (t) cc_final: 0.7752 (t) REVERT: B 308 MET cc_start: 0.8577 (ppp) cc_final: 0.8012 (ppp) REVERT: C 174 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7444 (tm-30) REVERT: D 167 MET cc_start: 0.7217 (tpp) cc_final: 0.6912 (tpp) REVERT: D 297 ILE cc_start: 0.8738 (mm) cc_final: 0.8402 (tt) REVERT: F 95 ASP cc_start: 0.8380 (t0) cc_final: 0.7822 (t0) REVERT: F 181 ARG cc_start: 0.6804 (tpm170) cc_final: 0.6561 (tpm170) REVERT: F 256 GLN cc_start: 0.8081 (tt0) cc_final: 0.7837 (tm-30) outliers start: 48 outliers final: 39 residues processed: 215 average time/residue: 0.1115 time to fit residues: 38.3837 Evaluate side-chains 218 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 153 THR Chi-restraints excluded: chain A residue 202 ASP 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 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 249 THR 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 174 GLN Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 70 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 22 optimal weight: 0.0010 chunk 116 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- 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** D 169 HIS ** D 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 = 0.4220 r_free = 0.4220 target = 0.136788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.094206 restraints weight = 35842.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.094666 restraints weight = 30856.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094553 restraints weight = 27012.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094665 restraints weight = 26942.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094853 restraints weight = 25834.379| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16391 Z= 0.149 Angle : 0.626 13.022 22529 Z= 0.311 Chirality : 0.040 0.185 2517 Planarity : 0.004 0.049 2553 Dihedral : 17.427 178.054 3065 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.77 % Favored : 91.17 % Rotamer: Outliers : 2.65 % Allowed : 21.07 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.21), residues: 1711 helix: 1.23 (0.21), residues: 556 sheet: -2.67 (0.21), residues: 531 loop : -2.12 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 177 TYR 0.017 0.001 TYR A 120 PHE 0.032 0.002 PHE C 234 TRP 0.047 0.002 TRP C 306 HIS 0.003 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00340 (16385) covalent geometry : angle 0.62526 (22517) SS BOND : bond 0.00278 ( 6) SS BOND : angle 1.54211 ( 12) hydrogen bonds : bond 0.03304 ( 662) hydrogen bonds : angle 4.40009 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7850 (p90) REVERT: A 325 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7217 (t80) REVERT: A 330 VAL cc_start: 0.8033 (t) cc_final: 0.7755 (t) REVERT: B 308 MET cc_start: 0.8555 (ppp) cc_final: 0.8006 (ppp) REVERT: C 174 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: C 309 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8360 (tp) REVERT: D 167 MET cc_start: 0.7293 (tpp) cc_final: 0.6997 (tpp) REVERT: D 297 ILE cc_start: 0.8743 (mm) cc_final: 0.8410 (tt) REVERT: E 66 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7549 (t80) REVERT: F 95 ASP cc_start: 0.8407 (t0) cc_final: 0.7815 (t0) REVERT: F 181 ARG cc_start: 0.6816 (tpm170) cc_final: 0.6569 (tpm170) REVERT: F 256 GLN cc_start: 0.8081 (tt0) cc_final: 0.7831 (tm-30) outliers start: 42 outliers final: 36 residues processed: 212 average time/residue: 0.1079 time to fit residues: 36.6136 Evaluate side-chains 217 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 153 THR Chi-restraints excluded: chain A residue 202 ASP 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 101 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 249 THR 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 174 GLN Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 HIS Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 325 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 154 optimal weight: 4.9990 chunk 75 optimal weight: 0.0050 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 172 optimal weight: 30.0000 chunk 133 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 44 optimal weight: 0.0370 overall best weight: 0.5074 ------------------------------------------------------------------------------- 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** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN F 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.139468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097112 restraints weight = 35669.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.097858 restraints weight = 29781.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.097955 restraints weight = 25912.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.098016 restraints weight = 26862.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098071 restraints weight = 25303.967| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16391 Z= 0.108 Angle : 0.621 12.875 22529 Z= 0.304 Chirality : 0.040 0.188 2517 Planarity : 0.004 0.053 2553 Dihedral : 17.355 177.105 3065 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.33 % Allowed : 21.77 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.21), residues: 1711 helix: 1.28 (0.21), residues: 561 sheet: -2.56 (0.22), residues: 530 loop : -2.16 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 181 TYR 0.034 0.001 TYR F 158 PHE 0.027 0.001 PHE C 234 TRP 0.042 0.002 TRP C 133 HIS 0.003 0.001 HIS F 131 Details of bonding type rmsd covalent geometry : bond 0.00242 (16385) covalent geometry : angle 0.62074 (22517) SS BOND : bond 0.00155 ( 6) SS BOND : angle 1.13144 ( 12) hydrogen bonds : bond 0.03184 ( 662) hydrogen bonds : angle 4.25079 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2919.13 seconds wall clock time: 51 minutes 20.88 seconds (3080.88 seconds total)